The World Health Organisation said evidence of a link remained inconsistent and urged caution in drawing conclusions.
Trump had on Monday linked autism to childhood vaccine use and the taking of Tylenol by women when pregnant, elevating claims not backed by scientific evidence to the forefront of US health policy.
The European Medicines Agency said on Tuesday there was no new evidence that would require changes to the region's recommendations for the use of paracetamol, known as Tylenol in the United States, during pregnancy.
"Available evidence has found no link between the use of paracetamol during pregnancy and autism," the EMA said in a statement, adding paracetamol could be used during pregnancy when needed, though at the lowest effective dose and frequency.
On Monday, Britain's health regulator said it was safe to use.
"The evidence remains inconsistent," WHO spokesperson Tarik Jasarevic told a Geneva media briefing on Tuesday when asked about a possible link between paracetamol use in pregnancy and autism.
He cited unspecified studies that pointed to a possible link but said this was not confirmed by subsequent research.
"This lack of replicability really calls for caution in drawing casual conclusions," he said.
In a highly unusual media conference at the White House on Monday, Trump delivered medical advice to pregnant women and parents of young children, repeatedly telling them not to use or administer the painkiller and suggesting that common vaccines not be taken together or so early in a child's life.
The advice from Trump goes against that of medical societies, which have cited data from numerous studies showing that acetaminophen, the active ingredient in Tylenol, plays a safe role in the well-being of pregnant women.
Asked to elaborate further on Trump's remarks, Jasarevic added that vaccines did not cause autism and affirmed their life-saving qualities.
"This is something that science has proven, and these things should not be really questioned," he said.
