The worst floods in decades battered seven big industrial estates in October at huge economic cost.
The flood impact, together with an increase in the daily minimum wage in April, means some operators could review their employment plans, cut jobs or close their business, the National Economic and Social Development Board (NESDB) said.
Industries that could see layoffs included cars, electronics, textile and garments, machinery, rubber, plastics, household goods and petroleum products, it said.
Unemployment in the fourth quarter was still low at 0.6 percent, or 245,890 people, much lower than the NESDB had expected, but it said that might not reflect the full impact of the flooding.
Some firms had decided to keep people on their payrolls because the labour market is tight and there is a shortage of skilled workers. In addition, various government measures have helped struggling companies retain staff.
The unemployment rate fell to 0.7 percent in 2011 from 1.0 percent in 2010, while real wages rose an average 2.8 percent last year.
The leading party in the government coalition had promised a rise in the daily minimum wage to 300 baht ($9.9) across the country before last July's election.
However, for now, that level has been set only for Bangkok and six other provinces, where wages were already relatively high, taking effect from April.
The rest of Thailand's 77 provinces will get a rise of around 40 percent in April, but that will leave the minimum wage under 300 baht..
The NESDB said the minimum wage for about 5.1-6.9 million workers was below the new rates, meaning employers would have to spend 6.7 to 11.1 billion baht ($221-$363 million) more on wages per month, another 6.2 to 10.2 percent.