Muslims travelling on trains from Brighton have objected to sniffer dogs being used to search them for drugs and bombs.
The trial by the British Transport Police (BTP) on all rail passengers travelling through the station prompted complaints from some Muslims who said their religion did not allow direct contact with dogs.
The findings, outlined in a Government report, showed that in another trial on the Heathrow Express platform at London's Paddington station, body scanners were considered unacceptable on religious grounds by female Muslims.
The report on five rail security trials conducted in 2006 and the public's response to them also revealed that some Asians and black people felt they could be selected for tests because of their ethnicity or because screening staff saw them as potential terrorists.
But the BTP said that despite being conscious of other people's beliefs, no-one would be absolved of the security checks on religious grounds.
A BTP spokesman said: "We are obviously aware of, and sensitive to, cultural sensitivities.
"BTP officers do have the power to stop and search anyone under section 44 of the Terrorism Act.
"This also covers the use of dog handlers and dogs, which are used to indicate any substance they have been trained to detect.
"As a force we obviously look at feedback about how people from all faiths and backgrounds view the use of dogs and how we can incorporate that into how the dogs and their handlers interact with people."