The budget bill was sent to the opposition-controlled upper chamber following its approval by the House of Representatives where the centre-left Democratic Party holds a vast majority.
The conservative Liberal Democratic Party and other opposition forces were opposed to a set of budget-linked bills which allow the government to issue new bonds worth 44.2 trillion yen for the year beginning on April 1.
The issuance of fresh bonds will aggravate Japan's massive public debt, which at nearly double its gross domestic product is the worst among industrialised nations.
But even if the House of Councillors rejects the draft budget, it will be enacted on April 6.
Decisions by the lower house have priority in case of conflict with the upper house and automatically become law 30 days after being sent to the upper chamber.
Prime Minister Yoshihiko Noda's government is considering formulating a stop-gap budget to cover the first weeks of the new fiscal year as the budget and related bills are seen as unlikely to pass the upper chamber by March 31, the end of the current fiscal year, media reports said.
The proposed budget is technically 2.2 percent smaller than the original budget for the current year.
But local media said the budget in reality is the largest ever, worth more than 96 trillion yen, when key items accounted for in separate budgetary steps are included, such as money needed to rebuild Japan's northeast ravaged by a massive earthquake and tsunami in March last year.