Beltran, a five-time All Star who has collected three Gold Glove awards for his fielding prowess in center, missed the first half of last season after having knee surgery and played just 64 games.
The 33-year-old Beltran is still wearing a brace on his right knee and was not expected to play in spring training games in Florida for at least another week.
Pagan, who took over in center field during Beltran's absence, will assume the position on a full-time basis, the club said.
"When Carlos was on the disabled list they gave me the opportunity to fill his shoes," Pagan told reporters, according to Major League Baseball's official website (www.mlb.com).
"I was just trying to do my job out there, trying to help the team as much as I could, and I guess I did it well."
Pagan, 29, hit 11 homers, drove in 69 runs, stole 37 bases and batted .290 in his first full season as a starter.
Beltran, an outstanding baserunner in his career who swiped only three bases last season, admitted to Mets officials that he still felt limited by the injured knee.
"In my heart, I still feel that I can play center field," said Beltran, whose .255 batting average was his lowest in a decade. "But at the same time, this is not about Carlos. This is about the team."
(Writing by Larry Fine; Editing by Steve Ginsburg)