The claim, which has become the latest twist in Bulgaria's complicated saga of EU funding misappropriation, has also become a political battle between the new prime minister and his opponents.
Borissov's statement comes in the wake of a European Commission threat to pull the plug on environmental project funding unless the Bulgarian government adequately explains - by the end of January - how and where they are spending the money. The warning was written in a letter by the Commission's director-general of regional policy, Dirk Ahner, received by Sofia on 13 January.
In February 2009 and again in May the same year, the Commission sent letters to the Bulgarian environment ministry, saying there was a problem with money absorption under the programme and demanding an explanation for some unfairly expensive water and sewerage contracts, said Environment Minister Nona Karadjova, who took office after Borissov's right-of-centre party GERB swept into power in 5 July elections (EurActiv 06/07/09).
In June, at Brussels' request, the government launched an investigation into projects estimated to be worth roughly 100 million euros under the operational programme.
Government sabotage claims ring hollow
Karadjova said the two letters from the European Commission had been kept secret as they were not registered at the ministry's records, and she therefore had only learned about them later on.
Borissov went a step further, dubbing the "hiding" of the letters by the former cabinet as "sabotage".
Speaking to EurActiv, a Commission spokesperson for regional policy said that there were growing concerns about Bulgarian cohesion funds.
On 26 June 2009, the Commission sent a letter to Sofia calling for a proper investigation to be made, as procurement and open tender rules were not being properly followed in the environmental sector.
Half a year later the Commission is still waiting for a reply, and Borissov's government is saying that they were unaware of the letters.
However, the government's claims of ignorance ring hollow in Brussels, another Commission source confirmed. "The facts contained in Ahner's letter are well-known to the Bulgarian authorities, not only because they've been addressed in these letters but because they've been addressed in a number of technical meetings between the Commission and the managing authorities in Bulgaria."
Borissov's response is a ploy to buy more time, they said.
Borrisov failing to live up to Brussels expectations
Privately, EU officials are disappointed that Borissov has failed to live up to the lofty expectations he expressed when he swept to power.
When outgoing Regional Policy Commissioner Pawel Samecki first travelled to Sofia to meet Borissov after the new government had taken office, and met his counterpart, Regional Minister Rosen Plevneliev, he was very impressed by the new administration's determination to clean things up and get things done, one staff member said.
"Borissov was talking about a zero-tolerance policy where they wouldn't accept any failure in cleaning up regional funding management. This was a message that came across loud and clear, that it wouldn't be business as usual, but a new era of cooperation," the source says.
However, these latest setbacks have restored Bulgaria's image as the "problem child" of EU regional funding.
The other major concern, written in bold type in Ahner's letter, is that three years into the current seven-year (2007-2013) regional programming period, only 1% of funding has reached beneficiaries in Bulgaria, a result which "is definitely not sufficient to have an impact on the economy in a time of crisis".
"We are absolutely at the disposal of the Bulgarian government to help them, but we can't if they're not communicating" is the message from the EU executive.
If Sofia fails to respond by end-January 2010, the Commission will consider suspending Bulgaria's environment funds, meaning a cut of up to 20% in EU monies.