The Kam Air flight was abruptly forced to fly back from central Bamiyan province earlier this week, triggering uproar and ridicule on social media with many accusing the lawmakers of abusing their powers.
Five people, including airport security officials, have been arrested over the "illegal diversion", the interior ministry said Thursday.
"When the two MPs arrived at Kabul airport, the plane was on the runway and ready to take off," Humayun Stanakzai, a director of civil aviation, told AFP.
The plane carrying 30 passengers had to be refuelled and took off again for Bamiyan with the two MPs on board.
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The lawmakers, Abdul Rahman Shaheedani and Hussain Naseri, were not immediately reachable for comment.
Kam Air, a private carrier, on Wednesday said they were indefinitely suspending all flights to Bamiyan, adding that the incident could have risked the lives of the passengers and airport workers.
Civil aviation has been expanding rapidly in Afghanistan since the Taliban were ousted from power in a US-led invasion in 2001, with several private airlines operating in the country.
Flight safety remains a concern but aviation disasters are relatively rare in Afghanistan, where travel by road through vast and remote terrain is made more hazardous by the Taliban insurgency.