Several Ninh Binh players have been implicated in a match fixing scandal.
The club's decision leaves 12 teams left in the national premier league for the rest of the competition.
At the meeting in Ha Noi, they also decided that the bottom-placed team at the end of the season will take part in a play-off match against the third-placed team in the First Division for the right to play in the V-League next season.
Previously, the bottom team were automatically relegated.
Ninh Binh's withdrawal has also affected the championship table.
Ninh Binh played eight matches, winning one, drawing four and losing three.
The teams that beat Ninh Binh have been deducted three points, and as a result, Becamex Binh Duong have lost their position at the top of the table they secured last weekend.
Thanh Hoa have returned to the top with 23 points after 10 matches.
Hung Vuong An Giang, who drew 2-2 with Ninh Binh on March 28, lost one point and remain at the bottom of the table with just one point after nine matches.
Police prosecute Ninh Binh match fixing case
Ninh Binh Province Police will move ahead on plans to prosecute the Ninh Binh football club players embroiled in a recent match fixing case.
According to reports, nine players from the team discussed and illegally bet VND1.02 billion (US$48,600) on a match against Malaysian side Kelantan during the Asian Football Confederation Cup on March 18.
Their team won 3-2 and the players pocketed VND800 million ($38,000).
The cash was then divided among the players who competed in the match, who earned VND85 million ($4,000) and the substitutes who took home VND75 million ($3,500). Around VND70 million ($3,300) was given to two who were complicit in the act but did not participate.