The Federal Government has ruled out supporting a Senate inquiry into the Church of Scientology.

Last month Independent Senator Nick Xenophon called for an inquiry into the church and its tax-free status after raising allegations of criminal conduct by the church.

Senator Xenophon told Parliament he had received letters from former followers detailing claims of abuse, false imprisonment and forced abortion.

"I am deeply concerned about this organisation and the devastating impact it can have on its followers," he told the Senate.

"Do you want Australian tax exemptions to be supporting an organisation that coerces its followers into having abortions? Do you want to be supporting an organisation that defrauds, that blackmails, that falsely imprisons?

"Because on the balance of evidence provided by victims of Scientology, you probably are."

But a spokesman for Government Senate Leader Chris Evans says it is not the role of Parliament to inquire into those matters.

He says the Government believes the allegations should be dealt with by the Taxation Commissioner and police.

At the time of Senator Xenophon's allegations, a spokeswoman for the church, Virginia Stewart, said she was shocked to hear the claims, as no-one within the church seemed disgruntled.

Ms Stewart said the church tried to contact Senator Xenophon earlier this year after he spoke about Scientology on television but "he didn't even bother to reply".