"I hadn't done anything criminal - otherwise I would've been in a court not in illegal detention," he told the BBC.
At a press conference in January, a spokesman for Pakistan's powerful military said it had had nothing to do with the disappearance of the bloggers.
Pakistan's interior minister had previously said the government did not tolerate "enforced disappearances".
After Waqass Goraya and the other activists disappeared, a campaign demanding their release sprang up around the hashtag #recoverallactivists. But a counter-campaign both online - and backed by a number of TV anchors - accusing them of blasphemy also began.
Blasphemy is an emotive issue in Pakistan - and can legally be punishable by death.
Mr Goraya says the allegations of blasphemy are false, and that alleged blasphemous postings have been fabricated.
Following a court petition by an Islamist leader, on 8 March legal proceedings were begun calling for the prosecution of those behind a number of social media pages allegedly run by the missing activists.
All of them are now believed to be outside Pakistan. Pakistan's Interior Minister Chaudhry Nisar Ali Khan has previously raised concern about the blasphemy allegations against the activists - but following the court ruling threatened to block "all social media websites" that had blasphemous content.
Mr Goraya believes the blasphemy allegations are an attempt "to shut us down - to threaten our families - to build pressure on us".
A protest was held in Islamabad on 8 March by religious groups calling for action against the activists and criticising the government for letting them leave the country.
Mr Goraya says he believes that by speaking to the UN, he can help build pressure in Pakistan to pass a bill currently before parliament that would force the security services to provide information on a "missing person" in their detention within three days of a request.
He also wants accountability for what happened to him.
"The government should investigate it. We have evidence - strong evidence - it will directly lead to the persons responsible."
Mr Goraya still has nerve damage in his hands and feet, as well as problems with his hearing - but says he is determined to continue activist work.
"They are still picking people, more and more people are being harmed - our friends, our colleagues - so how can we stop? Someone has to stand up."