A leaked phone call between the EU foreign affairs chief Catherine Ashton and Estonian foreign minister Urmas Paet has revealed that the two discussed a conspiracy theory that blamed the killing of civilian protesters in the Ukrainian capital, Kiev, on the opposition rather than the ousted government.

The 11-minute conversation was posted on YouTube – it is the second time in a month that telephone calls between western diplomats discussing Ukraine have been bugged.

In the call, Paet said he had been told snipers responsible for killing police and civilians in Kiev last month were protest movement provocateurs rather than supporters of then-president Viktor Yanukovych. Ashton responds: "I didn't know … Gosh."

The leak came a day after the Russian president, Vladimir Putin, said the snipers may have been opposition provocateurs. The Kremlin-funded Russia Today first carried the leaked call online.

The Estonian foreign ministry confirmed the leaked conversation was accurate. It said: "Foreign minister Paet was giving an overview of what he had heard in Kiev and expressed concern over the situation on the ground. We reject the claim that Paet was giving an assessment of the opposition's involvement in the violence." Ashton's office said it did not comment on leaks.

During the conversation, Paet quoted a woman named Olga – who the Russian media identified her as Olga Bogomolets, a doctor – blaming snipers from the opposition shooting the protesters.

"What was quite disturbing, this same Olga told that, well, all the evidence shows that people who were killed by snipers from both sides, among policemen and people from the streets, that they were the same snipers killing people from both sides," Paet said.

"So she also showed me some photos, she said that as medical doctor, she can say it is the same handwriting, the same type of bullets, and it's really disturbing that now the new coalition, that they don't want to investigate what exactly happened."

"So there is a stronger and stronger understanding that behind snipers it was not Yanukovych, it was somebody from the new coalition," Paet says.

Ashton replies: "I think we do want to investigate. I didn't pick that up, that's interesting. Gosh," Ashton says.

Russia Today, reporting the call, said: "The snipers who shot at protesters and police in Kiev were allegedly hired by Maidan leaders, according to a leaked phone conversation between the EU foreign affairs chief Catherine Ashton and Estonian foreign affairs minister, which has emerged online."

Last month, a recording was leaked in which US state department official Victoria Nuland was heard venting the White House's frustrations at Europe's hesitant policy towards pro-democracy protests. Speaking to the US ambassador to Ukraine, Geoffrey Pyatt, Nuland was heard to say "fuck the EU."

Asked about the emergence of a second embarrassing phonecall, a spokesperson for the US state department said: "As I said around the last unfortunate case, this is just another example of the kind of Russian tradecraft that we have concerns about."