The Red Cross says the buildings were clearly marked
This is the second time ICRC buildings have been hit since US air strikes began on 7 October. Two of the warehouses hit this time were struck last time around.
The US admitted accidentally bombing ICRC warehouses in Kabul on 16 October, injuring a security guard, but said that Taleban vehicles had been seen in the area.
"Although details are still being investigated, preliminary indications are that the warehouses were struck due to a human error in the targeting process," it said in a statement.
There were no immediate reports of casualties.
"It has happened again," said Mario Musa, spokesman for the International Committee of the Red Cross (ICRC).
"Huge explosions took place and three of our warehouses are on fire now."
Mr Musa told the BBC the compounds hit on Friday contained food, blankets and other material that was to be distributed to thousands of disabled and needy people in the city.
He said all Red Cross installations were clearly marked and all parties in the conflict had been told their locations.
Loss of life 'regretted'
He said the bombing took place at 1130 local time on Friday (0700 GMT) in good visibility.
The French news agency AFP also reported that two girls - sisters aged six and 11 - were killed when a US bomb landed on a village on the outskirts of Kabul early on Friday.
The United States has repeatedly said it is not targeting civilians and regrets any loss of life.
Officials at a Kabul hospital told AFP a man also died when a bomb hit a communications centre in the east of the city on Friday.
Taleban claims refuted
The deaths came a day after the United Nations confirmed that nine people had been killed when a US cluster bomb landed near a village in western Afghanistan on Monday.
The Taleban claim that more than 1,000 civilians have died nationwide since strikes began, but the US accuses them of inflating the figures.
Taleban troops are reported by the UN to be moving into residential areas to make it harder for US warplanes to strike them without hitting civilians.