It was the first such apology from Mr Salmond as First Minister and came a week after it emerged that Holyrood has lost the 3p single variable rate (SVR) tax power for at least the next three years.
But the SNP leader told MSPs he wanted "urgent" talks with Prime Minister David Cameron amid concern over the impact over the proposed Calman tax-raising powers in next week's Scotland Bill.
A difficult week for John Swinney was capped as the government lost a Holyrood vote over last week's Budget proposals, amid opposition concern that they are only for one year.
The finance secretary had already apologised to MSPs on Wednesday for not informing parliament about the decision to withhold payments to HMRC to maintain the upkeep of the so-called "tartan tax", which allows ministers to raise - or lower - income tax by 3p.
This apology was echoed by Mr Salmond yesterday as he came under pressure from opposition leaders at First Ministers Questions.
"I believe John Swinney was right to apologise to the parliament for not bringing these matters for parliamentary decision," he said.
"I join in that apology."
However, Tory leader Annabel Goldie said Mr Salmond's apology was "less than convincing".
Labour leader Iain Gray branded the SNP administration an "incompetent shambles" and said ministers had "secretly stopped spending money on a tax power this parliament should have". But the First Minister insisted the SVR was "not in a workable condition" when the SNP came to power in 2007, adding: "It would have taken many millions of pounds to implement it."
The UK coalition government is due to publish the Scotland Bill next Tuesday, which is expected to include radical new tax-raising powers for Holyrood. These would see income tax in Scotland effectively cut by 10p, with the Scottish Government then responsible for putting it back up to the level required, in line with need.
But Mr Salmond said ministers now knew the content of the bill and he had written to David Cameron to demand "urgent talks", amid concerns about the cash shortfall Scotland faced.
The original Calman proposals would have left Scotland 900 million worse off in 2009-10 had they been in place, the SNP claims.
The government also suffered a Holyrood reverse over its one-year Budget for 2011-12, which was branded "stop-gap" after being published last week by Mr Swinney.
• Commenting on this article has been suspended due to violations of our terms and conditionsA motion was backed calling on the government to bring forward its spending plans for the next four years.
Labour deputy leader Johann Lamont said: "If Mr Swinney is to win back the confidence of MSPs, he needs to accept the will of parliament and bring forward a full four-year spending review, as ministers have done in Wales and England."
Pressed to deliver more than a one-year plan, Mr Swinney said: "The government has done exactly what it's required to do, in terms of parliamentary process, which is to propose a draft Budget, because Parliament only ever discusses and debates one-year's Budget provisions."