Women officers must write down their "detailed menstrual history and history of LMP [last menstrual period] including date of last confinement [maternity leave]," the form says.
Women working in the civil service told the BBC the government had no need for this kind of personal information.
"I am completely shocked!" said Sharwari Gokhale, environment secretary in western Maharashtra state.
"I have absolutely no words to describe how I feel and I have no intention of telling them anything about my personal life.
"It's gob smacking."
Ms Gokhale said she had also served in the personnel department at the ministry which drafted the new forms and, while the health of officials was always a concern, asking such questions never crossed their minds.
Maharashtra's joint secretary for general administration, Seema Vyas, agreed that the new questions were uncalled for.
I assume this will help evaluate the officer's fitness
Satyanand Mishra, Personnel department secretary
"Menstrual cycles are a natural phenomenon, they are not an aberration. One does not object to questions related to fitness levels - they are important as they can affect work.
"But there is no need for these details as this does not have any bearing on our work," she told the BBC.
"When we apply for maternity leave, we put in the appropriate application and the government already has those records so why ask again?"
There are some things that employers don't need to know and this is one of them
She said she and her colleagues were thinking of writing a letter to the authorities protesting at the questions.
Despite repeated attempts, the BBC was unable to speak to the head of the personnel department, Satyanand Mishra.
The Hindustan Times newspaper quoted him as saying the questions were based on advice from the Ministry of Health.
"We sought the ministry's help to draw up a health-history format. I assume this will help evaluate the officer's fitness," he told the paper.