Spot-fixing is where the outcome of minor aspects of a game is fixed, for example the number of wides or the score on an individual ball.
Khan told the BBC: "I think spot-fixing is very much prevalent and really something you cannot prevent.
"This is opposed to match-fixing which requires the whole team."
Khan, who resigned following Pakistan's forfeiture of the Oval Test against England last August in a row over ball-tampering, said he would be very surprised if the current Pakistan team was involved in the throwing of an entire match.
He was speaking amid suggestions Pakistan coach Bob Woolmer was murdered because he was about to reveal allegations of match-fixing.
Woolmer was strangled to death, the day after Pakistan were knocked out of the World Cup after a shock defeat to Ireland.
Khan, who was also a personal friend of Woolmer's, also told the BBC: "Bob never shared with me any doubts about match-fixing.
"But this makes me feel that if something happened on that score it must have been after he left Pakistan for the Caribbean and during the two matches we lost to West Indies and Ireland.
"But I know this team and I do not think they would engage in match-fixing. They were the most morally upright team that I came across."
Meanwhile, the police chief heading the investigation into the murder of Woolmer told a British Sunday newspaper that the odds on Ireland beating Pakistan would be probed.
Mark Shields, Jamaica's deputy commissioner of police, raised suspicions over generous odds of eight to one being touted for an Irish win in the hours before the Pakistan match, The Observer reported.
Rumours have swirled that the strangling murder of the 58-year-old former England Test player may be linked to match-fixing gangs suspecting he was soon to blow the whistle on corrupt practices.
Shields told The Observer: "One aspect is what were the odds on Ireland if Ireland won. I understand that they were extremely good if you bet on Ireland. The match-fixing thing is being looked at."