Joshi, whose house was searched by CBI yesterday, claimed that he was "being pressurised and threatened by Additional Secretary in the Home Ministry B K Prasad to give clean chit to some of the NGOs", which he had refused to obey.
Prasad, who is heading the Foreigners Division handling NGOs and issues related to Foreign Regulation Contribution Act, denied the allegations levelled against him.
"The case is with the CBI and its the most competent organisation. I am sure truth will come out. Whatever Joshi is talking is rubbish," Prasad said.
Joshi claimed that Prasad had "verbally" asked him to give favourable comments on Ford Foundation "which I refused. Soon, he ensured that I am transferred out of Foreigners Division.
"I demand that the CBI should investigate B K Prasad. There should be an investigation why clean chit was given to Ford Foundation," Joshi said.
Prasad, a Tamil Nadu cadre IAS officer, had joined the Home Ministry in June 2014 and is due to retire on May 31.
Joshi claimed that CBI has not found anything from him and denied that he had taken any file to his home.
"All files were found in the Home Ministry itself. It can be verified after checking the CCTV cameras. It is a conspiracy against me. I have given adverse opinion against many NGOs including Greenpeace, Ford Foundation and two NGOs of Teesta Setalvad," he said.
Joshi said he was given offer of crores of rupees to give clean chits to NGOs which he always refused.
He claimed that despite being honest he was being framed.
"There is no corruption charge against me. They have not found any disproportionate property," he claimed.
Meanwhile, CBI today opened the lockers of Joshi at ICICI Bank's Indirapuram branch in Ghaziabad, the sources said.
They said Joshi has been called tomorrow for questioning.