The time begins when you enter the country , not the vehicle. This is very important to keep in mind. At the end of three months, you have the may extend this for an additional three months. If you wait until the three month period is up, you are required by law to pay the taxes on the vehicle. Do not drive the vehicle if the permit has expired.
Any vehicle being driven after the permit has expired is considered an abandoned vehicle.
The police have the right to confiscate the vehicle permanently. Before shipping the vehicle, take the license plates off the vehicle and either carry them down with you or ship them with a mail carrier. Plates are often stolen during transport or when the vehicles arrive. Thieves use the stolen plates to place on cars stolen within Costa Rica. If you are pulled over and cannot produce the documents, they will detain you and impound the vehicle.