The new sites will have access to food and basic shelter
Mr Kessler said priority would be given to inhabitants of the Killi Faizo camp near Quetta in southwest Pakistan and the Jalozai camp near Peshawar.
The Pakistani Government, which has only allowed a tiny proportion of Afghans fleeing the US-led attacks to cross the border, gave permission for the move on Thursday.
According to the latest UNHCR figures, more than 135,000 Afghans have entered Afghanistan since the 11 September attacks, virtually all of them illegally.
'Most desperate of the desperate'
The UNHCR has had the new sites ready for some time but has been hampered by Pakistani Government opposition to their dispersal.
"We have identified three sites in Baluchistan province and eight in North West Frontier Province and we are expecting to start moving them on Saturday," Mr Kessler was quoted as saying.
"The people there are the most desperate of the desperate. They need assistance and some kind of protected status. They need the benefit of being in a safer place," he told AFP.
Killi Faizo is just 600 metres from the Afghan border and there have been reports of Afghanistan's Taleban militia intimidating its inhabitants.
The UNHCR has said it was greatly encouraged by the decision to allow the 3,000 mostly women and children to move.
The makeshift camps at Jalozai and Killi Faizo lack even the most basic amenities and have become notorious for their appalling conditions.
Mr Kessler said the inland sites were still "pretty basic" but were far more secure and had accessible supplies of tents and food, unlike the appalling.
Closed border
Humanitarian agencies believe it is unlikely Pakistan will open its borders to all Afghan refugees.
Only the most desperate have been going to stay in the makeshift camps, while the rest have gone to live with friends or relatives.
Aid agencies fear for the thousands who have crossed illegally into Pakistan, either by using clandestine routes or by bribing border guards.
The UNHCR said it hoped these so-called invisible refugees will also be allowed to stay in the new refugee camps, but some aid workers say there should be guarantees that they will not simply be deported.
The agency believes some 75,000 have entered the North West Frontier Province and 60,000 have crossed into southwestern Baluchistan.
Mr Kessler said previously there were supplies for 200,000 refugees in Pakistan, but fear of deportation was preventing many of them from coming forward.
The UN estimates that around 5 million people in Afghanistan are in need of immediate humanitarian assistance; 100,000 children may die this winter if aid does not get to them soon.