As long as oil gushed from Pemex’s giant offshore fields, there seemed little reason for anyone to challenge the status quo. But production has declined since 2004, and the company’s ability to find and exploit new sources of oil has been cast into doubt.

The commission has closely tracked the Chicontepec project, on which Pemex has already spent nearly $9 billion. The regulators told the company that in its haste to meet ambitious production goals, it was drilling hundreds of new wells without studying the region’s geology or the best recovery techniques.

The criticism was quickly picked up by members of Congress.

Mr. Zepeda is also scrutinizing Pemex’s plans to push deeper into the Gulf of Mexico. The memory of the BP disaster there in 2010 is still fresh, and Mr. Zepeda is concerned that Pemex does not have enough experience to drill three new exploratory wells at depths of almost 10,000 feet — more than twice the average depths it has been drilling in the region.

David Shields, an independent oil analyst based in Mexico City, said the change in approach was significant. “It was heresy in the past to question whether Pemex was doing things properly,” Mr. Shields said. The commission’s five members all had previously worked for Pemex or for government entities involved in energy. But their decisions have shown independence, said Miriam Grunstein, an oil specialist at the CIDE, a public research university in Mexico City.

“They have integrity,” Ms. Grunstein said. “They’re really admirable. It’s completely unexpected.”

In the last few weeks, Pemex and the chief of its production and exploration subsidiary, Carlos Morales Gil, have begun responding to the pressure. The company officially reduced its estimate for probable reserves in Chicontepec by about 30 percent, to 6.49 billion barrels of oil equivalent, ending two years of wrangling with Mr. Zepeda’s team.

Then, at the end of March, Pemex announced that it had signed a contract with Wild Well Control, a Houston company that handles oil well disasters, including the 2010 BP spill, to provide deepwater containment systems, and it is in talks with a consortium of gulf oil companies to provide additional services. Pemex is also analyzing whether it should buy additional insurance for the deepwater wells, Mr. Morales said.