He said the government shared the widely held view that war graves should remain undisturbed and protected.
Launching the three-month project in Orkney, Junior Defence Minister Lewis Moonie said the day of the wrecker had passed.
A law passed 14 years ago to give sunken naval ships the status of official war graves has never been applied.
In unveiling details of the consultation paper in Kirkwall, Dr Moonie paid tribute to survivors' associations who have thrust the issue into the limelight.
He said the government shared the widely held view that war graves should remain undisturbed and protected.
The consultation paper will now be circulated to diving groups and survivor associations.
The minister was told about the HMS Royal Oak which was torpedoed by a German U-boat with the loss of 833 lives at Scapa Flow, off the Orkney coast, on 14 October 1939.
The minister placed a wreath at the Royal Oak memorial and met representatives from the Orkney branch of the Royal British Legion.
The ship, which is an official maritime war grave, is carefully protected by the local council, but hundreds of other vessels dotted round the UK coastline do not enjoy the same protection.
There has been increasing public concern that wrecked navy vessels are being disturbed and plundered by some divers.
The government has decided to step in, and over the next three months it is seeking people's views on how to better to safeguard them.
The Royal Oak was carrying over 70 tanks of oil when she was hit, which would have meant a maximum load of 3,400 tonnes.
Although much of this was lost when the ship sank, the remaining fuel - now estimated to be around 1,800 tonnes - is escaping from the wreck.
Orkney Islands Council is worried the oil could now be escaping at the rate of 1.5 tonnes per week, threatening the local environment.
After the failure of two attempts to stop the flow using containment methods, the Royal Navy unveiled a new scheme last October, which will see as much of the oil as possible being removed.
A method known as "hot tapping" is to be used, which involves valves being attached to the wreck to suck the oil out.
He said it was hoped divers would be able to go down at some stage over the next few days to begin the process.
The project is being funded by the Ministry of Defence, and after being brought to the surface the oil will be taken away for environmentally friendly disposal.
Mr Willmot said the operation might not succeed in removing all the oil from the wreck, but it should remove the bulk of it and therefore end the risk of large-scale leaks in future.
"We are doing it once and for all to remove the risk of a large scale oil incident," said Mr Willmot.