Responding to queries related to Jet Airways, including possible bailout package, Prabhu said that in a deregulated atmosphere, the ministry's endeavour is to deal with sector-specific issues.
"For a private airline, it is for the airline's board of directors, their management to make sure that the airline functions properly and they have to take appropriate measures depending upon market conditions that will prevail from time to time," the minister said.
However, he did not directly mention Jet Airways.
While emphasising that the ministry is very clear about taking up aviation sector specific issues, Prabhu cited the example of pitching for bringing aviation fuel under the Goods and Services Tax (GST).
Civil Aviation Secretary R N Choubey said the airline wanted some more lead time with regard to payments to airport operators but that was something to be done commercially between the two entities.
"That is something that they have to deal with airport operators. The ministry does not get into that.
"We don't get into commercial discussions between airlines and airport operators. It is to be done commercially between the two entities," Choubey said.
They were speaking at the sidelines of an event here.
On November 13, cash-strapped Jet Airways said it is at various stages of discussions with multiple "interested parties" for capital infusion and partial stake sale in its loyalty programme Jet Privilege.
The airline is looking for investors to tide over the liquidity crisis, which has resulted in delayed payments to some vendors and salaries to a section of its over 16,000 employees.
On November 16, Tata Sons confirmed its interest in acquiring the beleaguered Jet Airways but said no concrete "proposal" has been made by the group so far.
Earlier in the day, an airline source said that Jet Airways' pilots have threatened not to perform additional duties from next month if their salary dues were not cleared by November 30.
Meanwhile, Prabhu said there would be zero tolerance on aviation safety-related issues. "We have asked the DGCA to carry out safety audit of all airlines... strict safety audit," he added.
The DGCA is the aviation regulator.
Shares of Jet Airways declined nearly 7 per cent to close at Rs 323 on the BSE.