Salvors are still cleaning up what is left of the cargo and the ship, which came apart and finally sank earlier this year.
Crown prosecutor Rob Ronayne told the court today the crew made a catalogue of errors while racing to the Port of Tauranga under time pressure.
He said the ship cut corners and sailed hazardously close to other landmarks and the captain and navigational officer tried to cover up their faults.
There were "substantial deviations'' from the approved passage plan without just cause.
Most seriously, Balomaga instructed Relon to later plot a false chart position at 2am on October 5 - 15 minutes before the Rena ran aground - so that it gave the appearance of the Rena passing clear of the Astrolabe Reef, Mr Ronayne told the court.
When interviewed on October 11, neither man mentioned falsifying the charts.
Balomaga also admitted a charge under the Resource Management Act of being the master of a ship from which harmful substances or contaminants were discharged into the coastal marine area, and also pleaded guilty to four charges under the Crimes Act of wilfully attempting to pervert the course of justice.
Relon also pleaded guilty to three similar charges, which relate to altering ship documents after the grounding, and a charge under the Resource Management Act relating to the discharge of harmful substances and/or contaminants.
The sentences related to the Crimes Act and Maritime Transport Act charges. There was no imprisonment over the RMA charges.
After the sentencing, Rena owners Costamare said it would continue to meet its responsibilities as their employer to ensure their welfare and that of their families
"The Rena owners and our insurers continue to be closely involved in managing the response to the grounding, especially through the activities of our salvage and recovery teams. There are many complex legal, environmental and community issues still to be resolved from the grounding and we are committed to working with all affected parties to achieve a satisfactory conclusion.''
In a separate prosecution, a charge laid under the Resource Management Act by Maritime New Zealand against Costamare's subsidiary, Daina Shipping, was adjourned without plea until July 18.
MNZ director Keith Manch welcomed the sentencing, which held the two officers to account for their failures in relation to the incident.
"This grounding has had significant consequences for the Bay of Plenty community and the country as a whole. Today marks a milestone in the response, which is still under way.''
Mr Manch said MNZ was supported in its investigation by the Bay of Plenty Regional Council, police and other parties including the Port of Tauranga, local iwi and the local community.