The 90-day interval starts from the date the car was registered.
Car owners who fail to observe the deadline will be fined and will have registration plates removed.
The decision was taken to make sure Romanians who register their cars abroad will pay the car registration tax in Romania.
According to the Romanian Police, Romania has about 19,800 cars registered in Bulgaria, out of 45,000 vehicles registered elsewhere, including Italy, Spain and the UK.