The charging document says Clifton made "an oral statement that he knew to be false" on June 26 last year, which allegedly helped Smith to get a passport.
But Clifton said he never expected Smith to leave the country.
"If he didn't do this he would have got out," he said.
Clifton said he called police immediately after hearing the news that Smith had left New Zealand.
Clifton was 18 when he met Smith in Mangaroa Prison, now Hawkes Bay Regional Prison.
He was doing two years for assault with intent to commit robbery with a weapon.
Clifton was addicted to drugs and said that while they were in prison together Smith helped clean him up.
"He treated me nicely. I had a lot of people trying to beat me up and make me do certain things I didn't want to do - he protected me and looked out for me.
"He never gave me a reason to hate him."
Clifton knew Smith was in for murder, but wasn't initially aware of the sexual convictions.
"You don't just walk up to somebody in prison and go 'what are you in for?"'
When he eventually found out about the sexual offending he said Smith played it down and told him he'd been about 17 and in a gay relationship with a 15-year-old boy. It was only after Smith's escape from New Zealand that Clifton found out the true facts.
"I don't condone any of this," he stressed. "I have a family to protect. Don't get me wrong, he's a bad guy that's done some horrible shit."
However, Clifton believed there was "decency in everyone" and nobody was bad "to the core".
Clifton went to live with Smith's sister when he was released from prison, and would attend Smith's parole hearings and drive Smith's family members to the hearings.
Since appearing in court this week, Clifton said he had received "50 million calls" as well as threats on Facebook.
He said he had been offered name suppression and turned it down - "It was going to come out.
"I'm not going to run from this, I'm not going to try and hide from this."
Clifton's next court appearance is in Wanganui on January 20.
Smith was also in court in Auckland this week and his next court appearance was originally set for February but defence lawyer Tony Ellis sought a delay until March.