Resident priest Hartmut Borries said there was no one available who could carry out her role if she had to leave.
Ms Tomanek had completed the church's theological training in Stuttgart, Germany, and was also a qualified teacher.
"The 180 or so students at the two Rudolf Steiner schools here will be without a religious education teacher and our church will be without a very able leader," said the Rev Borries.
"Andrea has been responsible for all of the church's education programme in Auckland, covering not only children and youth but also adult religious education."
The Christian Community, founded in 1922 in Switzerland, has about 30 to 40 regular followers in Auckland. But Mr Borries said special services can bring about 100 to 150 to the church.
Unlike most other Christian churches, members do not need to conform to any specific teaching or behaviour.
Immigration spokeswoman Rachel Purdom said Ms Tomanek's position as a minister's assistant meant a large part of what she did involved secondary or supporting duties.
Religious worker visas were introduced in November but religious work must substantially be a primary role for the applicant.
"Ms Tomanek's position cannot be considered an offer of religious work ... a religious instruction teacher can be regarded as a religious worker, but only if the teaching position is substantially a primary role," Ms Purdom said. "In Ms Tomanek's case, the information provided does not indicate that her primary role is that of a religious instruction teacher."
According to Immigration's trends and outlook report, 10 people had been granted residence under the category since its implementation.
Ms Tomanek said she would not consider a further work visa, as it would not allow her 20-year-old dependent son to remain here with her. "I am also not able to afford to pay the $19,000 fees for him to continue studying at the University of Auckland."