Jacob Juma was driving home from a bar to his home in an upmarket suburb on Thursday night when unknown gunmen attacked his car.
Police said they escaped on motorbikes after firing 10 shots at the vehicle.
Mr Juma, who had mining interests, had been involved in several high-profile legal cases against the government over failed business deals.
"We don't know the motive but this seems to be a pure murder," Nairobi police chief Japheth Koome is quoted by Kenya's Standard newspaper as saying.
Police say nothing was stolen from the businessman, as two of his mobiles were found in his car along with some cash.
The BBC's Odhiambo Joseph in Nairobi says he had sued a state corporation, seeking about $5m (£3.4m) in compensation for a breach of contract to supply 40,000 tonnes of maize in 2004.
He had also taken the government to court in 2015 for revoking his company's mining licence.
Cortec Mining Kenya had claimed it had identified mineral deposits worth billions of dollars in the coastal county of Kwale.
The businessman had also been critical of the governing Jubilee Coalition on how it has tackled corruption and was supportive of opposition leader Raila Odinga, our reporter says.