Shortly after Cookson was elected UCI president in Florence during a spectacular congress - - the Ethics Commission, the guardian of the ethical principles of the UCI's Code of Ethics, was subject to a major overhaul.
Dutchman Peter Zevenbergen, who brought up claims against Russian Igor Makarov, one of the biggest supporters of Cookson in his election campaign, was asked to leave his job, he claims.
"It is quite simple: the new management committee did not accept my criticism," Zevenbergen told Reuters on Tuesday.
Article 14 of the Code of Ethics of the UCI state that the members of the Ethics Commission "shall be irremovable", unless they die or resign.
"I think those who were in the congress meeting last year would have been disappointed with the performance of the Ethics Committee as it was represented, Cookson told reporters on Tuesday.
"I think that it was quite clear that we had to change. We have got a new ethics commission now, all the members of the commission have been renewed. People we have are of the highest quality."
Zevenbergen said that he received a visit from Martin Gibbs, the UCI director general, in late December, 2013, as the Ethics Commission was investigating claims that Russian federation president Makarov had promised one million euros ($1.36 million)to the Union Europenne de Cyclisme (UEC) in exchange for a Cookson vote.
"Martin Gibbs came to Amsterdam to discuss this with me on the 27th of December. I would not say he asked me to resign, there was some pressure, he said he did not want to continue with me.
"He said if I stayed, it (the Ethics Commission president job) would be an empty function.
"As a consequence Peter Barth from Germany resigned from the commission."
Sources told Reuters that Barth, who left his job in April, felt the independence of the Ethics Commission could not be guaranteed anymore.