(BBC) -- Rory Stewart said converts to Isis believed in an "extremely hateful doctrine" and had moved away from any allegiance to Britain.
They can expect to be killed because of the "serious danger" they pose to the UK's security, he said.
The government said his comments were in line with the UK's stated position.
Mr Stewart made the remarks after Brett McGurk, a top US envoy for the coalition fighting Isis, said his mission was to ensure every foreign fighter in Syria dies there.
Asked about the comments on BBC Radio 5 Live's Pienaar's Politics, Mr Stewart, a former diplomat, said they were "very difficult moral issues".
He said: "They are absolutely dedicated, as members of the Isis, towards the creation of a caliphate.
"They believe in an extremely hateful doctrine which involves killing themselves, killing others and trying to use violence and brutality to create an 8th Century, or 7th Century, state.
"So I'm afraid we have to be serious about the fact these people are a serious danger to us, and unfortunately, the only way of dealing with them will be, in almost every case, to kill them."
Mr Stewart's comments contrast with the independent reviewer of terrorism legislation, who recently told the BBC that Britons who join Isis through "naivety" should be spared prosecution if they return home.
Max Hill QC said UK authorities should instead look at reintegrating such people.
A government spokesman said Mr Stewart's remarks were consistent with the position set out by Defence Secretary Sir Michael Fallon on 12 October.
Sir Michael said British Isis fighters in Syria and Iraq had made themselves "a legitimate target" who could end up on "the wrong end of an RAF or USAF missile".
His comments came after it was reported that British Isis recruiter Sally-Anne Jones had been killed in a US drone strike in Syria in June.
The head of MI5 revealed this month that more than 130 Britons who travelled to Iraq and Syria to fight with the terror group have died.
Mr Stewart also said British authorities had made it "very clear" that people should not be volunteering with militia groups to fight against Isis.
(Photo: Getty)