Rusty streaks were clearly visible around the base of the spire of the stupa, whose outer part is made of gold in the shape of an inverted lotus.
Concerns of possible damage to the much-revered stupa have been widely aired by social networkers. The stupa was recently cleaned of mould and fungus and given a fresh coating with a type of cement solution.
Among those expressing concern for the stupa was former education minister Samphan Thongsamak.
Samphan urged officials to take action, saying all Buddhists were worried about the stupa, built in the early 13th century.
Samphan said it was unprecedented for the stupa to develop such rusty leaks.
Officials at the 14th Fine Arts Department Office in Nakhon Si Thammarat said the base of the spire was last repaired in 1992.
A gold section in the shape of two linked lotuses was removed for cleaning and refitted with bricks, fibreglass, tin and stainless steel to replace its wooden core, which had rotted.
Anat Bamrungwong, director of the 14th Fine Arts office, said he had instructed officials to use a special camera to check the base of the spire and report back to him as soon as possible.
He said a full commission of experts from the Fine Arts Department would have to consider the findings and decide on a course of action to fix the stupa.