Yingluck said the damage had already been fixed.
"It was not a structural problem."
The airport was closed for repairs after an area of 3,600 sq cm at the northern part of the western runway was found to have subsided by 5cm about on Thursday night, delaying a number of flights and diverting 11 others.
Yingluck said the runway defect was caused by normal wear and tear.
Heavy use of the western runway following the closure of the eastern one could have also contributed to the damage.
She said the damage would not compromise safety standards.
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"Actually it is normal because Suvarnabhumi airport has been in use for several years. The number of flights has exceeded expectations, shortening its use," she said.
According to Suvarnabhumi management, the airport has handled about 1.5 million flights since it opened in September 2006.
The Don Mueng airport, which served as the former international airport, will now be used by budget airlines.
The airport was affected in last years floods but has been repaired and is functional.
However, critics have called into question whether the construction of the Suvaranabhumi airfield met required standards, Bangkok Post said.
Piyaman Techapaiboon, president of the Tourism Council of Thailand, has urged AoT to speed up its plan to construct the third runway.
The third runway is scheduled to be completed in 2017.
She urged the AoT to begin a feasibility study into a fourth runway to accommodate a larger number of flights.