New 'anti-terror laws' have allowed the government to deregister the groups, freeze their bank accounts and remove the work permits of foreign employees.
The measures were introduced after an increasing number of attacks from Islamist militants at the al-Qaeda-linked al-Shabab group.
Last month Al Shabab killed 64 people, mostly Christian, in two separate attacks.
Muslim extremists shot dead 28 non Muslims on a bus
But the new laws faced fierce criticism and at one point sparked a punch fight in the Kenyan parliament.
Henry Ochido, the deputy head of the government-appointed NGO Co-ordination Board, said the NGOs had lost their position because they had failed to submit financial records.
He told the BBC 15 of the 510 were suspected of money-laundering and financing "terrorism," but he refused to name them.
Many people in Kenya fear the government is using the threat posed by militant Islam to restrict freedom.
The AFP news agency says many of the charities are Christian although it's understood none are from the UK.
Fazul Mahamed, the executive director of the board, told Kenya's privately owned Standard newspaper: "The NGOs with accounting issues can only be allowed to operate if they successfully go through a thorough vetting process. Otherwise, they will remain deregistered indefinitely."