Haneef has been in detention in Brisbane since July 2, when he was picked up by police at the international airport trying to leave the country on a one-way ticket to India.
Australian police on Friday decided not to seek extention of Haneef's custody, media reports said.
His extended detention over the foiled car bombings in London and Glasgow has been criticised by the Law Council and civil libertarians for being an abuse of anti-terror powers.
Asked if he was uncomfortable with the 11-day-long detention Howard said, "No, I am not," TV channels reported.
He said Australians were entitled to have effective laws to fight terrorism.
"There are all the safeguards in the world under these laws. People can't be held without the authority of a judicial officer," Howard said adding "the question of whether he is a terrorist or not is a matter to be decided by the police in the first instance and then by the courts.
"I'm not calling him a terrorist, I'm not passing judgment on him and I'm not going to pass a judgment on the process he is subjected to at the moment' he said.