Parishioners have apparently complained of having to park next to the grave, which, adorned with a cross and covered in candles and flowers, occupies a space in the car park.
The local Catholic Church in the south-western town of Swiebodzice, Poland, said it had decided to allow the burial in the car park as it was on church land, and that it was an appropriate resting place for the deceased, Father Zenon Kowalski.
"The choice of burial site for Father Zenon was taken in accordance with the wishes of the deceased's family, the parish council and a large number of the faithful," said Father Lukasz Ziemski, a spokesman for the local curia.
"Father Zenon helped build this church and this is where he belonged."
But prosecutors were called in following complaints that the grave is breaking laws restricting burial to cemeteries.
While their investigation continues the local health and sanitary inspectorate made clear that it had no doubts that the car-park resting place was illegal.
"The law is clear: the dead can only be buried in cemeteries," said an exasperated Halina Madra, a spokeswoman for the inspectorate. "We explained this to the curia and the mayor, but the burial still went ahead."
The adamant statement indicates that Father Zenon's resting place may not be his last, and that his remains will have to be exhumed and reburied in a cemetery.
Church authorities said they would respect any exhumation order.