The drugs have been used by up to one in six women of child-bearing age.
A manufacturer contacted by the BBC denies any link to major foetal malformations.
Panorama has spoken to eight mothers who had babies born with serious heart defects after taking a commonly used SSRI (selective serotonin reuptake inhibitors) antidepressant while pregnant. Currently, prescription guidelines for doctors only warn specifically against taking the SSRI, paroxetine, in early pregnancy.
But Prof Pilling, of the National Institute for Health and Care Excellence (NICE), says that advice is about to be updated.
"The available evidence suggests that there is a risk associated with the SSRIs. We make a quite a lot of effort really to discourage women from smoking or drinking even small amounts of alcohol in pregnancy, and yet we're perhaps not yet saying the same about antidepressant medication, which is going to be carrying similar - if not greater - risks," he said.
When Anna Wilson, from Ayrshire, had her 20-week scan, doctors realised her son had a serious heart problem and would need immediate heart surgery when he was born.
David will need further surgery before he starts school
Now eight months old, David was hooked up to machines for the first five weeks of his life. He will need more open-heart surgery before he starts school and doctors say he may not live beyond 40.
"He's got a lot of suffering ahead of him before anything else," his mother said. "We know that's a certainty and that's pretty awful."
Four years before she became pregnant, Mrs Wilson was prescribed the drug Citalopram by her GP because she was suffering from anxiety.
Her doctor told her it was fine to continue using the drug when trying for a baby. But after David was born she asked what might have caused his heart condition.
"We did meet with a cardiologist at one of the scan appointments, and he explained that as far as he knew there were no environmental factors and it wasn't because of anything we as parents had done. It was just one of those things - couldn't be prevented," she said.
Prof Pilling says the guidance will now be re-written to take in to account evidence that the SSRI antidepressants, as a group, are linked to heart defects.
He says the risk of any baby being born with a heart defect is around two in 100; but the evidence suggests if the mother took an SSRI in early pregnancy that risk increases to around four in 100.
Professor Stephen Pilling: "I don't think those risks are really worth taking"
He says that women not suffering from the most severe depression who become pregnant whilst taking the drug are taking an unnecessary risk.
"You've got double the risk. And for women who are mild to moderately depressed, I don't think that those risks, in most cases, are really worth taking" he said.
"It's not just when a woman who's pregnant is sitting in front of you. I think it needs to be thought about with a woman who could get pregnant. And, that's the large majority of women aged between 15 and 45."
Mrs Wilson will never know for sure what caused David's heart defect, but said if she had known there was even a very small risk associated with the drug she would have stopped taking it.
"If David's condition was preventable, and it wasn't prevented, that's really, really awful.
"If somebody had given me the choice in pregnancy and said 'there's a risk of this', I would have stopped taking those tablets in a flash."
Lundbeck, the manufacturer of Citalopram, says a recent review of scientific literature concluded that the drug "does not appear to be associated with an increased risk of major foetal malformations".
"The decision not to prescribe anti-depressants to a woman who is depressed... may generate greater risks to the woman and her foetus than the risks of exposure to the medication."
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