Ahmed Muthana told BBC TV his son Nasser, 20, from the Welsh capital Cardiff, was one of five Islamist fighters who appeared in the video released this week encouraging others to join ISIL and fight for it in Syria and Iraq.
The video comes amid growing concern among British police, security services and political leaders about the number of Britons travelling to Syria and becoming radicalised by militant Islamists.
"I want to cry. Why are you doing this? Who led them to go there?" said Muthana of his medical student son, who appears in the online footage identified as Abu Muthanna al-Yemeni from Britain.
"Is he going to kill or is he going to do anything?"
The BBC said Muthana, who told them his 17-year-old son Aseel had also gone to Syria, had been radicalised in Cardiff.
"I don't think that's Nasser talking, it's someone else is teaching him to talk like this because the attitude of Nasser is 100 percent completely different," he said.
"Somebody is driving those kids to do this problem."
ISIL, an offshoot of al Qaeda, has captured swathes of territory in northwest and central Iraq, including the second city of Mosul, taking weaponry from the fleeing Iraqi army.
On Saturday, security sources said the Sunni militants had seized a border post on the Iraq-Syria frontier.
British Prime Minister David Cameron said on Wednesday ISIL was currently the greatest security risk to Britain and fighters who travelled to Syria and Iraq posed a real threat to the nation on their return.
Peter Fahy from Britain's Association of Chief Police Officers told the BBC an estimated 500 Britons had gone to Syria and Iraq.
The broadcaster said two men who are believed to have travelled with Nasser Muthana to Syria had previously been arrested in Britain on suspicion of terrorism offences.
South Wales Police issued a statement saying two men, aged 19 and 23, from Cardiff, had been held on suspicion of receiving terrorist training.
"The arrests, which were made in March and April this year, related to travel to Syria and took place when the men returned to the UK," the statement said.
"Following consultation with the Crown Prosecution Service, both men have been released without charge."
Two years ago a group of men, some from Cardiff, were jailed for plotting to bomb the London Stock Exchange as part of a campaign of al Qaeda-inspired attacks across the British capital in the run-up to Christmas 2010.