The decree came in response to a proposal received from Prime Minister Algirdas Butkevičius on Tuesday evening.
The decree will take effect on June 3. Justice Minister Juozas Bernatonis has been appointed as acting minister of economy.
On Tuesday, Butkevičius said Minister of Economy Birutė Vėsaitė would work until next Monday, also pledging to search for a new candidate for the post.
He also added that the Chief Official Ethics Commission's conclusions on Vėsaitė's potential conflict of public and private interests would not have influence on her staying in the office.
"A decision has been made that the economy minister made a mistake. We definitely cannot talk about certain categorical public accusations against her. She just made a mistake and did not think about the flight on the private jet. The final decision has been made that she will work until the upcoming Monday," Butkevičius told the Lithuanian national radio LRT on Tuesday.
Vėsaitė came under fire last week after she and her two advisers flew to a business forum in Kazakhstan on an eight-seat business-class plane chartered by Arvi, a Lithuanian company. The round-trip flight of the three officials cost 8,100 litas (EUR 2,345), or 2,700 litas per person, while civil aviation specialists say that such a business-class charter flight to and from Astana may cost about 100,000 litas, or about 13,000 litas per passenger.
Arvi is currently holding negotiations with the Economy Ministry over Marijampolė free economic zone (FEZ) operation contract. The Chief Official Ethics Commission will decide on an investigation into the incident next Tuesday.
The Lithuanian president, Grybauskaitė, said on Monday that the Prime Minister should look for a replacement for Vėsaitė.