Royal Marines special forces are in Afghanistan
American and British troops, including members of the elite Special Boat Service (SBS), have secured the key Bagram airbase near the Afghan capital, Kabul.
They are preparing the base for aid flights and possible military operations, and thousands of British Paras and Commandos could begin flying in over the weekend.
Mr Hoon dismissed reported Northern Alliance complaints they had not been consulted, telling the BBC's World At One programme: "We have been in contact with the Northern Alliance.
"The situation on the ground is pretty chaotic for the moment.
"We believe they will recognise the benefit of having experts on the ground who can tell them and us what needs to be done in order to make the air strip at Bagram usable for the kinds of humanitarian and diplomatic missions that clearly are going to be necessary."
Focused mission
Meanwhile, Foreign Secretary Jack Straw has vowed British troops will have a focused mission and will not be drawn into a wider conflict.
The SBS will only be preparing the ground for more troops by checking for mines, and will assess the possibilities for humanitarian aid.
The SAS has already been operating in Afghanistan for some time, and the SBS is the Royal Marines' equivalent service.
Downing Street said the forces were under direct British command, but working through the US general field headquarters.
The soldiers were drawn from "high readiness" troops kept in the region after the recent UK exercise in Oman.
The prime minister's official spokesman told reporters on Friday the coalition's position was much better than a week ago.
But he argued: "This isn't unfolding like a Stephen Spielberg script.
"You are going to have problems along the way which you are going to have to face up and deal with."
Some Royal Marine Commandos and members of the Parachute Regiment could also be deployed by the end of the weekend, says BBC defence correspondent Paul Adams.
But Mr Straw told BBC Radio 4's Today programme that UK troops would continue to have a specific mission and would not become involved in a civil war.
Campaign aims
He said the more general aims of any Western troops would be find Osama Bin Laden and topple al-Qaeda.
But the foreign secretary admitted British troops could find themselves sucked into a "conflict that was not anticipated".
Bagram airport, situated about 10 miles north-east of Kabul, is considered to be of key strategic importance.
As well as the British troops, 60 French soldiers were travelling to Uzbekistan on Friday, before heading on to Mazar-e-Sharif to help the aid effort there.
The UK is also sending its first diplomat to Kabul since 1989, following the withdrawal of the Taleban regime.
A Ministry of Defence spokesman said although many British troops were on standby, "there is no assumption yet that they are definitely going to be deployed".
Thousands of UK troops will remain on 48-hour standby to go to Afghanistan, MoD sources said.
These are said to include the 2nd Battalion The Parachute Regiment, the entire 45 Commando of the Royal Marines, and elements from 16 Air Assault Brigade and 3 Commando Brigade.
Mr Blair has said they could be used in future offensives against the Taleban, although protecting humanitarian supplies and "stabilising" work would be the priority.
He said with Taleban resistance largely broken, the chances of ensuring a stable future government in Afghanistan had improved dramatically.