The General Conference Mennonites Church plans to go to the Supreme Court, if necessary, to secure the right to disregard its obligation as an employer to collect employe income taxes that will be used for military purposes.

In a week-long meeting here, the church, with 600,000-members, told its officer to initiate such a suit.

In keeping with a long-standing tradition, the church also said that its members could legitimately refuse to register for the draft to show their opposition to war.

Church administrator, Robert Hull, indicated that approximately 10 percent of Mennonite draft-age men will not register. He counseled those who plan to register but want to show their opposition to military service to write on the registration card, "I am a conscientious objector to war in any form" as a record of their position.

A petition from an employe in the denomination's central offices in Newton, Kan., led to the proposal for the tax suit before the triennial meeting of church representatives from the United States and Canada.

In 1977, Cornelia Lehn, one of the church's specialists in Christian education, asked that her full salary be paid directly to her, so at income-tax payment time, she could withhold the percentage that would be spent on the military. Though church leaders were sympathetic, they felt at the time that they were obligated by law to continue withholding her taxes.

The Mennonites expect that the Church of the Brethren, the Religious Society of Friends (Quakers), and the Mennonite Church, a related denomination, will join in their suit.