Meetings at military units this week will review current codes of conduct on issues ranging from visits to military bases, the use of smartphones in bases, the prevention of sexual abuse and the management of firearms and other equipment, the defence ministry said.
"President Ma has asked the defence ministry to adopt concrete measures to tighten the discipline of the military so as to restore the public's faith in it," Ma's spokesman Charles Chen said in a statement.
He was found last week to have illegally brought a group of 26 civilians - most of them his rich relatives and friends - to the northern Lungtan base late last month.
The visitors toured an off-limits hangar and climbed into the cockpit of the helicopter to pose for photos, according to local media.
The case came to light when photos - showing a woman sitting smiling in the cockpit and her husband wearing a pilot's helmet - were seen on her Facebook page.
Lao was removed from his post as a pilot and faces a serious demerit while four other officers were also disciplined.
But that did not allay public anger. The United Daily News in a commentary blasted the armed forces.
"Discipline is the soul of troops. Could troops without discipline still have combat capabilities?" it asked.
Prosecutors in the northern city of Taoyuan launched an investigation into the case over the weekend.
In another case an army commander at Tungying, a Taiwan-administered frontline islet facing China's Fujian province, was removed from his post and placed under investigation last week following complaints by lower-ranking soldiers of sexual abuse.
It is a legacy of decades of tensions with China, which still regards the island as part of its territory after the two split at the end of a civil war in 1949.
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