It is understood the worm disabled the NavyStar network in up to 75 per cent of the navy's ships last week, meaning sailors could not get messages home.
The navy's flagship HMS Ark Royal, which left Portsmouth for Liverpool on Monday, is still without the system as IT technicians tackle the problem.
Sailors in the Portsmouth-based carrier have been relying on their mobile phones to contact loved ones when they have enough signal.
A sailor said: 'It has been utter chaos.
'They have let us use our phones but there are dozens of jobs which need the internet, and what about those people who are away on deployment?
'There are also cadets who joined the ship to head to Liverpool, and because they couldn't get e-mails they couldn't check how many people were coming on board.'
Portsmouth South MP Mike Hancock, who sits of the Commons Defence Select Committee, said: 'It is truly frightening to think that a virus can spread this far and this fast through the network.
'It was an expensive system to build for what is supposed to be one of the most secure sectors.
'It will also be a big blow for morale as e-mail has been an important step forward for sailors' welfare in the past decade.'
A Ministry of Defence spokesman confirmed that NavyStar was still out on several fleet ships, but insisted that the problem had not affected weapons or navigation.
He said: 'Since the problem was discovered priority has been given to repairing the system in deployed ships.
The vast majority of that has been done, but NavyStar is not yet working in Ark Royal.
'But the weapons and navigational systems remain unaffected by the virus, because they are on a separate system with higher security.
'Action was immediately taken to isolate the infected systems and commence virus-cleansing procedures to protect from re-infection.'
News of the virus comes as the Public Accounts Committee today criticised the Ministry of Defence in its report on the Defence Information Infrastructure.
On the issue of data security, the report said: 'The Department currently has an undesirable record on data security when it should be amongst the best in government.'