According to an audit report of Shri Ram Janmbhoomi Teerth Kshetra, a trust set up by the Centre for the construction of the temple, said the cheques bounced due to lack of funds in bank accounts or some technical error, news agency PTI reported.
Trust member Dr Anil Mishra said banks are working to solve the issue of technical errors and they are asking people to make donations again.
Among the cheques, around 2,000 were collected from Ayodhya.
The Vishva Hindu Parishad (VHP) had collected donations during a countrywide campaign between January 15 and February 17.
Around Rs 5,000 crore was collected during the drive though the final figures are yet to be declared by the trust.