Scottish Enterprise has received £50m from ministers to cover a £25m overspend the agency made last year.
Scottish Enterprise will decide how to spend its budget on Friday
Enterprise Minister Nicol Stephen announced the move and in a letter to agency chairman Sir John Ward sought assurances over efficiency.
The agency's board will meet on Friday to decide how the cash will be spent.
The Convention of Scottish Local Authorities (Cosla) condemned the move and said councils did not approach ministers with overspend problems.
Scottish Enterprise will be allowed to keep £5m of money it generates from property or investments.
The Scottish Executive will then underwrite it by £45m and allow the agency to dip into its own cash reserves.
This will give Scottish Enterprise an annual budget of £550m for this year.
Its board is due to meet on Friday to agree the budget and decide how the money will be spent.
In a letter to Sir John, the minister warned the agency it must improve its performance.
"You must manage your programme consistent with that figure for the rest of the year," he said.
"I hope that the board will take into account the expectations of partners and the need to explain clearly the considerations you have addressed in reaching a budget allocation.
"I will also want to be assured that your spend on administration has been tightly scrutinised and reduced, and that the budget set will allow you to meet legal commitments."
'Get a grip'
Cosla president Pat Watters said: "With the demands Scotland's local authorities have on our services, every council in Scotland could be going to the executive on a daily basis with overspends but we don't.
"Because we are accountable we live within a budget and we try to manage that budget - but hey, maybe it's us who are wrong."
Scottish Tory enterprise spokesman Murdo Fraser urged the enterprise minister to "get a grip".
"We need more clarity from the minister as to where this £50m is coming from? Which budget will be cut," said Mr Fraser.
"The minister needs to get a grip of his department and tell us what programmes are being cut."
Labour Central Fife MSP Christine May said she believed Scottish Enterprise should be administered efficiently.
"However, the important policy question for us is what is the right economic policy for Scotland and, for me, it is about setting the strategic priorities in energy and biotechnology, about maximising opportunities," she added.
SNP Aberdeen North MSP Brian Adam said he was seeking assurances from the minister over proposed cuts to the Skillseekers programme.
Shiona Baird, Green MSP for North East Scotland, said the manner in which Scottish Enterprise tackled its funding problems would be crucial for its credibility.
"If it makes cuts to funding of vital services like Skillseekers and modern apprenticeships, it will lose considerable support from the companies who need their skills," she said.