They found that women taking Prozac and Seroxat during the second and third trimesters increased the chance of their child having autism by 87%, compared to mothers who did not take any medication.
However Ian Dale, head of research at the National Autistic Society said parents should not panic, as the risk is still small.
Dale told HuffPost UK Parents: "This large study reveals potentially useful information about the possible risks of taking antidepressants during pregnancy.
"However, statistics can be tricky to understand, and while an '87% increased risk' sounds worrying, this would mean that mothers taking antidepressants would still have less than a two in 100 chance of having an autistic child."
The study, which followed 145,456 pregnancies, found 1,054 of the children involved were diagnosed with autism at an average age of four and a half years old.
The risk of this diagnosis was 87% higher if the mother had taken antidepressants during pregnancy, than for children whose mothers did not take antidepressants while pregnant.
Researchers took into account a variety of factors, including genetic predisposition to autism, maternal age, depression and certain socioeconomic factors.
They said the reason for the increased risk is unknown, but it was "biologically plausible" that taking the medication could interfere with the development of the unborn child's brain in the womb.
Professor Anick Bérard, who was involved in the research, said, according to the Telegraph: "Our study has established that taking antidepressants during the second or third trimester of pregnancy almost doubles the risk that the child will be diagnosed with autism by age seven, especially if the mother takes selective serotonin reuptake inhibitors, often known by its acronym SSRIs."
Dale added: "The reliability of the study has been questioned by the scientific community.
"As the authors have stated, the causes of autism are complex and not fully understood.
"Any mothers-to-be who are concerned should discuss their treatment with their doctor. No-one should make any decisions based on these findings alone.
"While it is important to understand the causes of autism, we believe more research needs to be focused on what helps autistic people and their families to have a good quality of life."
The NHS currently states taking antidepressants during pregnancy "isn't recommended".
NHS guidance states: "As a precaution, antidepressants aren't usually recommended for most pregnant women, especially during the early stages of a pregnancy.
"However, exceptions can be made if the risks posed by depression (or other mental health conditions) outweigh any potential risks of treatment."
Dr Helen Webberley, GP for www.oxfordonlinepharmacy.co.uk, said while the study does raise questions, pregnant women on antidepressants need to consult their doctors before making any changes.
"However it is vital we weigh up the risks and benefits both for the mother and the unborn child.
"With many medications the risks to the foetus may be perceived as very small, and the mother may need that medication for her own mental or physical health.
"It is not clear whether this study set out to establish a risk between antidepressants and autism, or whether this was an incidental finding, and clearly more research needs to be done into this emotive area.
"With every case, the doctor and the pregnant woman should sit down and discuss the pros and cons of taking any medication.
"In some cases of depression it is clearly better and safer for the mother to continue with her medication while she is pregnant."
Dr Webberley said many women do take antidepressants while pregnant, yet autism remains rare.
She added: "The risks associated with medication also vary depending on what stage the pregnancy is at and between different clinical cases and each case needs to be discussed individually.
"I would be very concerned if pregnant women suddenly stopped their medication as a result of this news, without fully discussing it with their doctor."