The ministry is asking for 180.5bn yen ($2.1bn, £1.3bn), some of which an official said would be spent on missile interceptors and fighter jets.
The move comes with Japan embroiled in a territorial row with China.
It also follows North Korea's recent successful long-range rocket launch.
"We will request 180.5bn yen to be allocated to military spending from a stimulus package," a defence ministry spokesman told Agence-France Presse news agency.
He said that part of it would fund the purchase of PAC-3 surface-to-air anti-ballistic missile systems and modernise four F-15 fighter jets.
The defence ministry spokesman said the funds were needed "to prepare for the changing security environment surrounding Japan".
The finance ministry has to approve the request before it can be added to the government stimulus package expected later this month.
Q&A: China-Japan islands row
The request for funds is in addition to news on Tuesday that the new government, which won elections in December, would increase the defence budget request by more than 100bn yen.
Officials say the increase would be used for research into a new radar system and maintenance costs for military aircraft.
The mooted increase is not large - the defence budget for the year ending in March 2012 stood at 4.65 trillion yen - but it represents a change.
For 10 years, Japan's defence budget has been gradually declining. But in the last few months the country has been shaken from two sides, says the BBC's Rupert Wingfield-Hayes in Tokyo.
In December, North Korea successfully launched a long-range rocket that flew over southern Japan. Much more worrying for Tokyo is China's push to claim disputed East China Sea islands, our correspondent adds.
The dispute over the islands, called Senkaku in Japanese and Diaoyu in Chinese, has rumbled for years.
Japan controls the islands but its purchase of three of them from their private Japanese owner in September sparked a renewed row.
Since then Chinese ships have been sailing in and out of what Japan says are its territorial waters around the islands, prompting warnings from Tokyo.
New Prime Minister Shinzo Abe, who is known as a conservative, has pledged a strong stance on the territorial issue while also calling for dialogue with China.

The man was wearing headphones as he worked in his home in Westfield Street in Heckmondwike, West Yorkshire, when the attacker struck on Wednesday.
He managed to call police when he regained consciousness and nothing was taken from the house.
Police said he was hit on the back of the head and treated in hospital for a minor head injury.
Any witnesses are urged to contact police.

The Scottish Gamekeepers' Association said the latest employment figures showed the sector was outperforming other areas of the economy.
North Highland College in Thurso reported that every one of this year's Higher National Certificate students has secured a job on a sporting estate.
Country sports are thought to be worth Â£240m a year to the Scottish economy.
The gamekeeping and wildlife management course was designed to provide students with training in conservation as well as traditional gamekeeping skills, including snaring and the use of firearms.
North Highland College gamekeeping lecturer Richard MacNicol said: "The modern gamekeeper has to have a rounded, balanced approach to land management.
"Our graduates are helping to support the rural economy and a diverse, well managed countryside."
Borders College and Scotland's Rural University College in Fife also said the skills obtained by their students were proving valuable to landowners.
The Scottish Gamekeepers' Association has welcomed the news.
SGA chairman Alex Hogg said: "This is a major success story and the three colleges deserve immense credit.
"We are creating youth jobs at a time when the economy is faltering and young people, especially in remote areas, have few other opportunities."
There is real frustration amongst landowners and the gamekeepers they employ about the profession's image.
Political and media attention often focuses on cases of wildlife crime, most notably the illegal persecution of birds of prey.
Gamekeepers believe they do not get the credit they deserve for the stewardship of our countryside, while landowners argue the economic benefit of country sports is often overlooked.
They are hoping the new generation of gamekeepers being trained by Scotland's colleges will help change that.
Angus McNicol, of Cawdor Estates near Nairn, told BBC Scotland: "It's a highly-trained profession these days. It's very different to how things were in the past."
Japan's defence ministry says it is seeking more funds for military spending, a day after news the government would boost the defence budget for the first time in 10 years.
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A man knocked unconscious while he was doing DIY at his home came round to find racist graffiti on the wall.
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Colleges across Scotland are reporting strong demand from sporting estates for newly-trained gamekeepers.