Compromised personal details of at least 3,500 applicants to the Royal Marines, the Royal Navy and the Royal Air Force include National Insurance numbers, doctors' addresses, passport numbers and bank account information.
The MoD said in a statement that it is treating the loss of data with the " utmost seriousness".
The Association for Payment Clearing Services has been asked to watch out for unauthorised access to bank accounts, and the MoD has written to the 3,500 people whose bank details were stolen.
The theft took place in Birmingham on 10 January, and is being jointly investigated by the MoD and West Midlands Police.
The incident was not reported until 18 January to avoid compromising the investigation, according to the MoD.
A report in The Times suggests that the junior Royal Navy officer responsible for safeguarding the laptop could now face a court martial.
This latest security blunder is an indication that lessons have still to be learned from the child benefit data loss at HM Revenue & Customs in November last year, according to data security specialist Check Point.
"What will it take for organisations to understand the risks?" said Nick Lowe, regional director for Northern Europe at Check Point.
"The HMRC data leak happened two months prior to this theft, but apparently the personal data on the Royal Navy laptop was not encrypted despite the easy availability of such software."
A survey of UK companies by Check Point in November 2007 found that only 48 per cent used data encryption software, and that 65 per cent had no intention of changing IT spending priorities in light of the breaches.
"It seems that some companies are still saying that 'it cannot happen here'. This laptop theft shows that it can happen all too easily," said Lowe.
This is the latest data debacle to embarrass the government following HMRC's loss of two CDs containing personal data around 25 million people.
Defence Secretary Des Brown is due to make a statement to Parliament regarding the Royal Navy incident this week.
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