The airline's safety head has also been removed by the regulator.
When contacted, a senior Air Pegasus official said that it has already addressed the issues raised by the regulator and also submitted a report in this regard.
The move comes at a time when the DGCA is taking stringent action against airlines for any kind of violations that could put the safety of passengers in jeopardy.
A safety audit of the Bengaluru-based Air Pegasus, conducted in late April, showed serious safety violations by some of its flights, a senior DGCA official said on Friday.
It was noticed that some of its pilots violated norms as flights operated by them descended at a "higher rate" than prescribed under the standard operating procedure, he added.
This includes a flight operated on Bengaluru-Thiruvanathapuram.
According to the official, five pilots of Air Pegasus have been suspended for a time period varying from a week to few months and its safety chief has been removed from the post.
However, he did not disclose the number of flights where violations were noticed.
Taking note of the flagrant violations, DGCA has sent a warning letter to the top management of Air Pegasus.
In recent times, many domestic airlines have come under the scanner of DGCA for various safety violations. These include instances of aircraft flying with less fuel than the prescribed limit, a plane almost landing on the road mistaking it for the runway and pilots allowing cabin crew inside the cockpit during the flight.
"We have already taken corrective measures and submitted an action taken report to the DGCA," Air Pegasus Managing Director Shyson Thomas, said.
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