A trial scheme supplying free morning-after pills has had little impact on teenage pregnancy, a document obtained by BBC Wales suggests.
The Catholic Church is concerned that the morning-after pill is now freely available in Wales even to under-16s.
Research into a pilot project in Bridgend questioned whether it was "an appropriate use of NHS resource".
The Welsh Government said emergency contraception was not part of its strategy to reduce teenage pregnancy.
Health professionals told BBC Wales' Week In Week Out the risk of pregnancy was higher than with other contraception methods.
The research, written by a specialty registrar working for NHS Trust Public Health Wales, said: "Despite the increased uptake of EHC [morning-after pill] in Bridgend… the trend in conceptions for Bridgend was not significantly different to the rest of Wales."
It concluded: "As a public health initiative to tackle unwanted teenage pregnancy, consideration must be given to whether this is an appropriate use of NHS resource."
Following a rolling programme started in 2001, the morning-after pill has been available free from pharmacies throughout Wales since April. It is said to have a 95% success rate.
Dr Caroline Scherf, a consultant in sexual and reproductive health with the Cardiff and Vale University Health Board, said people were not made aware that the risk of pregnancy was still higher than with other methods.
"The pill as emergency contraception is preferable to nothing after unprotected sex, but there is still a very high chance they will end up pregnant," she said.
"I am concerned it doesn't get out, that message."
Monsignor Robert Reardon, of the Roman Catholic Archdiocese of Cardiff, told the programme he was concerned about the moral issue of supplying the morning-after pill to girls under 16 and without telling their parents.
"The morning-after pill demonstrates the separation of sexuality and… responsibility," he said.
"You're left with something that is devoid of its intention - a recreational activity, almost."
Charlotte Burgess, 15, from Swansea, who is happily pregnant herself, believed the scheme would have unintended consequences.
"I think handing pills over the counter is just encouraging teenagers to have sex... they think they've got to do it."
However, Swansea pharmacist Steve Newbury said he would not hand out the morning-after pill to anyone without a 20-minute private consultation and unless he was satisfied it was safe and appropriate to do so.
The programme says providing free morning-after pills through pharmacies, when fully rolled out, will cost up to £300,000 a year, money that will be found from existing NHS budgets.
In addition to the report on Bridgend, evidence from 10 other countries, including England, suggested that increasing access to emergency contraception did not reduce unintended pregnancy rates.
A spokesman for the Welsh Government said the availability of emergency contraception through pharmacies was "an important aspect of a comprehensive sexual health service but not part of our strategy to reduce teenage conceptions".
Week In Week Out is on BBC One Wales on Tuesday, 14 June at 2235 BST.