"I have had several conversations with the president on the issue of the disposal of the Grand Regency hotel. As I have indicated before, my conscience is very clear on the role of the treasury and specifically myself in this matter," he said.
Kimunya's resignation, if it is accepted by Mwai Kibaki, Kenya's president, would weaken the coalition cabinet.
The executive was formed earlier this year after deadly clashes broke out in the wake of a disputed general election in December.
Kimunya has been accused by his critics of having deliberately undervalued the hotel in a sale conducted by the government last month.
One cabinet minister mocked the sale price as not enough to cover the cost of the furniture inside.
A Kenyan subsidiary of a Libyan firm bought the hotel.
Kimunya's resignation comes after a vote of no confidence in the Kenyan parliament.
|Kenya's coalition cabinet could be affected by Kimunya's exit [AFP]
Leaked government documents suggest the hotel was sold for $28m, but Kimunya says a price of $45m was agreed.
Libyan officials say the sale was conducted with the knowledge of the Kenyan government but some cabinet ministers have dismissed that claim.
Kimunya is an ally of Kibaki, who remained president after the general election despite claims by Raila Odinga, his opponent, that he had rigged the vote.
The dispute over the presidency sparked ethnic violence that left at least 1,500 people dead and displaced hundreds of thousands.
Kibaki remained in his post in a power-sharing deal, while Odinga was made prime minister.
Observers say that the exit of a minister loyal to Kibaki could lead to a cabinet reshuffle.