WASHINGTON (Reuters) -U.S. Transportation Secretary Pete Buttigieg said on Monday he expected Boeing to cooperate in investigations by the Justice Department and National Transportation Safety Board into the Alaska Airlines 737 MAX 9 mid-air emergency on Jan. 5.

"We respect the independence of DOJ and NTSB doing their own work, but we're not neutral on the question of whether Boeing should fully cooperate with any entity - NTSB, us or DOJ. And they should, and we expect them to," Buttigieg told a press conference.

He said Federal Aviation Administration chief Michael Whitaker had made clear to Boeing that "they need to go through a serious transformation here in terms of their responsiveness, their culture and their quality issues."

Boeing said in response it "will continue to cooperate fully and transparently with all government investigations and audits, as we take comprehensive action to improve safety and quality."

Boeing shares closed down 3%.

The aircraft manufacturer said on Friday it believed during production of the Alaska Airlines MAX 9, required documents were never created that should have detailed the removal of the door plug that failed, resulting in a mid-air emergency.

Alaska Airlines said on Saturday it was "fully cooperating" with the Justice Department in its criminal investigation and it did not believe it was a target of the probe.

In the aftermath of the incident, the FAA grounded the MAX 9 for several weeks, barred Boeing from increasing the MAX production rate and ordered it to develop a comprehensive plan to address "systemic quality-control issues" within 90 days.

NTSB Chair Jennifer Homendy last week criticized what she termed Boeing's lack of cooperation and failure to disclose some documents, including on the door plug opening and closing, as well as the names of 25 workers on the door crew at the 737 factory in Renton, Washington.

"It is absurd that two months later we don't have it," Homendy said.

After Homendy's comments, Boeing provided the 25 names and said the NTSB had only sought the names on Saturday. She plans to send a letter to the Senate later this week detailing Boeing's cooperation to date.

The FAA's Whitaker said on Monday the agency and Boeing hope to define in the next 30 days the milestones the manufacturer must meet in order to increase the MAX production rate.

An FAA audit released last week found issues with Boeing's manufacturing process control, parts handling and storage, and product control.

"We're really focused on quality assurance process where there really are gaps," Whitaker said, citing issues like "having the employees have the right tools and training, having the right engineering drawings, and assembling the aircraft in the proper order."