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"The regime's resistance is not necessarily at an end," Hoon told a press briefing in London.
"In Baghdad itself as in other urban areas, coalition forces may well face a difficult and dangerous period of flushing out Iraqi forces, particularly the various groups of irregulars, thugs and fanatics who hang on to the coat tails of the regime."
Hoon was speaking as US forces plunged into the heart of Baghdad on Monday, targeting three palaces and other symbols of Saddam's regime.
"A number of Iraqi formations outside Baghdad may yet have to be defeated if they do not capitulate first," Hoon said.
He added however: "What is clear is that Saddam Hussein's regime is coming to an end and that a better future is in sight for the Iraqi people."
The defence secretary added that British troops were in the southern city of Basra "to stay".
A British officer told journalists in southern Iraq that the battle for Basra was "more or less over" as thousands of troops poured into Iraq's second largest city.
British soldiers moved into the centre of Basra on foot earlier in the day, seizing control of the main southern town's university from Iraqi militiamen, an AFP correspondent reported.
Meanwhile, Hoon reported that he had "strong indications" that "Chemical Ali", a cousin of Saddam who was blamed for a gas attack that killed thousands of Kurds in 1988, had been killed in an allied raid.
"We have some strong indications that he was killed in the raid conducted Friday night but I can't yet absolutely confirm the fact that he is dead. But that would be certainly my best judgement in the situation," Hoon told the London press conference.
British military spokesman Group Captain Al Lockwood earlier told CNN that "Chemical Ali", or Ali Hasan al-Majid, had apparently been killed in the air strike.
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