MOSCOW — Russia’s communications watchdog was locked in an intensive game of whack-a-mole on Wednesday with Telegram, the popular and highly secure messaging app, as its stuttering attempts to block the service inadvertently knocked out the websites of scores of small businesses.
Alexander Zharov, the head of the watchdog agency, Roskomnadzor, acknowledged that it had obstructed millions of IP addresses in an attempt to shutter Telegram. Roskomnadzor took that step after the company declined to provide encryption information, which would enable the agency to identify users and see the content of messages.
The watchdog agency was granted authority to block the app on Friday by a Moscow court. But the clumsy, unprecedented effort to follow through, which started Monday, caused a widespread outcry after the unintended consequences became apparent.
A member of the band Pussy Riot organized a small public protest. Edward J. Snowden, the former N.S.A. contractor who leaked American surveillance documents and now lives in Russia, expressed support for the company. Even some usually staunch Kremlin supporters called the ban misguided.
Internet experts in Russia saw a greater menace in the effort beyond Telegram, speculating that if the government succeeded in silencing the app with some 13 million Russian users, it might pursue bigger fish next.
Indeed, in his interview with the newspaper Izvestia published on Wednesday, Mr. Zharov said that Roskomnadzor planned to investigate Facebook before the end of the year.
“If you have a government agency being so brutal attacking Telegram, taking down millions of IP addresses, after that you can do what you want,” said Andrei Soldatov, one of the authors of “The Red Web,” a history of the Russian internet. “After they have faced this much heat, they can go after Facebook and Google.”
Telegram tried to thwart the blockage by shifting its service to two giant American web hosts, Google Cloud and Amazon Web Services, while at the same time repeatedly changing its IP address to skip ahead of Roskomnadzor.
In response, rather than chasing individual IP addresses — a unique set of numbers that identifies a computer, smartphone or other device connected to the internet — the watchdog agency elected to shut down enormous blocks of addresses, called subnets.
The collateral damage hit a variety of other sites, like Viber, another messaging app, as well as small businesses including a language school and a courier service, all of which suffered financial losses.
Volvo dealerships could not access their service records, according to press reports, and Kremlin museums had to suspend ticket sales. Roskomnadzor said it unblocked individual sites as soon as the agency became aware of a problem.
The Agora group of human rights lawyers, which represents Telegram in Russian courts, said in a statement that it had received 73 complaints about blocked websites. The organization planned to file a formal complaint with the prosecutor general’s office.
In addition to the virtual warfare, the two sides sparred publicly. Mr. Zharov told the independent Russian news outlet The Bell that his agency had been able to cut off one-third of the traffic to Telegram, while the company said the figure was 5 percent. The Bell suggested that traffic even rose on the day the initial blocks had been imposed.
Telegram has been sending messages to users encouraging them to use alternative means, including Virtual Private Networks, which effectively connect to the internet outside Russia, to evade the ban.
The app’s founder, Pavel Durov, who fled Russia after losing control in 2014 of VKontakte, the Russian version of Facebook that he created, sent a message to Telegram users saying that he would continue to engage in “digital resistance.”
His supporters included Mr. Snowden, who wrote on Twitter that resistance to the “totalitarian demand” for backdoor access to private communications “is the only moral response, and shows real leadership.”
Maria V. Alyokhina, a political activist and member of the Pussy Riot collective who has been jailed for previous demonstrations, helped to organize a protest that consisted of tossing paper airplanes outside the Moscow headquarters of the F.S.B., the secret police. She was sentenced to 100 hours of compulsory community service, according to Mediazona, a courtroom news agency.
The paper airplane is the corporate symbol of the Telegram app. The F.S.B. has been leading the effort in Russia to gain backdoor access to all private communications in Russia, saying it was necessary to combat terrorism.
The ban came into effect after Telegram lost a court case over demands from the Russian government that the company provide the means for intelligence agencies to read encrypted messages.
Telegram was widely used within the Russian government, including by President Vladimir V. Putin’s press office, to communicate with the public and the media. Some government agencies and press offices continued to use Telegram despite the ban.
Igor Lebedev, the deputy chairman of the Russian Parliament and the son of nationalist leader Vladimir Zhirinovsky, accused the government watchdog agency of “incompetence.”
“It targeted Telegram but hit Russian business,” he wrote on Twitter, saying it should be illegal to limit access to such popular sites. “We must defend Russian citizens from pointless bans!”
The Kremlin has also come in for criticism on several other fronts: It has suggested using older, slower apps as an alternative, especially one owned by a Putin crony; it shut down LinkedIn and managed to limit some access to Zello, a voice messaging app used to organize truck driver protests; and it finds itself accused of paying lip service to the idea that Russia should develop cutting edge technology while busily undermining Telegram, one of the few Russian I.T. brands to achieve global success.
Iran seemed to be following Moscow’s lead, with news agencies reporting on Wednesday that it would ban government organizations from using foreign-based messaging services including Telegram, which is extremely popular in the Islamic Republic. More than 40 million Iranians use Telegram, which played an important role in spreading information about antigovernment protests in December and January.
The office of the supreme leader, Ayatollah Ali Khamenei, an active Telegram user, said he had shut down his account to set the example. The decision was “in line with safeguarding national interests and removing the monopoly of the Telegram messaging app,” the ayatollah’s last Telegram stated, according to Iran’s government-run Press TV news website.
The Russian government has been trying for several years to force all communications giants to store their information on servers in Russia and to provide the security services back door access to analyze the data. It has also suggested that Russia might unplug from the global internet and create its own web.
Internet experts suggest that what the Kremlin really wants is leverage to order the internet platforms to remove things that it does not like.
“They want a hotline that they can pick up to call someone to do something,” said Mr. Soldatov. “It is a very Soviet approach.”
Follow Neil MacFarquhar on Twitter: @NeilMacFarquhar.
Oleg Matsnev and Sophia Kishkovsky contributed reporting in Moscow.