It fears the move could lead to the dissolution of the Pheu Thai Party, a source at the ministry said.
An electoral regulation prohibits the government from using state human and financial resources, both directly and indirectly, ahead of a snap election, the source said.
He said the credit guarantee for the BAAC could be viewed as a breach.
Caretaker Prime Minister Yingluck Shinawatra dissolved the House on Monday and called a general election for Feb 2, following a mass rally of anti-government protesters.
If the credit guarantee to the state-owned bank is crucial, the ministry will ask the cabinet and the Election Commission to consider it first, the source said.
The Public Debt Management Office recently provided a credit guarantee for the BAAC's bonds, but only 37 billion baht of 75 billion offered were sold as investors had several concerns.
Farmers who pledged rice to the government for the main crop are facing late payments from the BAAC as the bank refused to use its own liquidity to fund the programme without the National Rice Policy Committee's approval to widen the 500-billion-baht outstanding spending limit.
Another way to resume payments is for the Commerce Ministry to accelerate its rice sales.
BAAC executive vice-president Supat Eauchai said the bank will coordinate with related government agencies to seek measures to help 4 million farmers awaiting payments.
The caretaker government remains committed to selling rice stocks including new grain available from the 2013/14 harvest to prevent a glut.
The government is still responsible for selling state rice stocks, including the planned disposal of 500,000 to 1 million tonnes through the Agricultural Futures Exchange of Thailand, said Niwatthamrong Bunsongphaisan, caretaker commerce minister, after the National Rice Policy Committee's meeting yesterday.
The ministry needs to discuss with the Council of State whether a caretaker minister can approve rice auction sales. The contracts the minister already signed will still be valid and delivery should be honoured as usual.
Mr Niwatthamrong said negotiations to sell the government's rice stocks on a government-to-government basis with potential buyers such as Indonesia and Malaysia must be postponed.
The Foreign Trade Department reports the government sold 7-8 million tonnes of rice over the last two years through G-to-G contracts.
The government remains adamant its rice stock is 10 million tonnes, although industry sources estimate the amount is closer to 16-17 million tonnes.
The government has spent up to 680 billion baht in four harvest seasons over the last two years, but has sold only 135 billion worth of rice. It has allocated a further 270 billion baht to finance the 2013-14 main crop.
Buying started on Oct 1, and some 6.16 million tonnes of paddy were pledged as of last Thursday.
The rice committee was planning to convene a meeting to approve a temporary increase in the 500-billion-baht outstanding spending ceiling, allowing the BAAC to pay farmers who pledged their rice under the current main crop, running from Oct 1 to Feb 28.
The government already exceeded the limit for the scheme, so its payment to farmers has been delayed, upsetting some farmers who threatened to rally to accelerate payment.
But without a House of Representatives, the acting government has no mandate to temporarily raise the spending ceiling for the scheme.
The cabinet previously set a deadline to decide the outstanding spending limit for the end of this year.