PORTST. LUCIE, Fla. — Pedro Martinez pitched three perfect innings in his second rehabilitation start yesterday before allowing three runs in the fourth.

Martinez, who has been working his way back from right shoulder surgery in October, threw 60 pitches for the Mets’ Rookie-level Gulf Coast League team and then another 20 fastballs in the bullpen.

“I like this outing a lot more than the other one,” Martinez said. “I am more in command, and I actually felt like I pitched a little bit, making pitches where I wanted to, and overall it was a jump ahead. It was a great improvement.”

Last Wednesday, the three-time Cy Young winner struggled through three innings and was pulled before reaching his target pitch count, allowing five runs and six hits in a Class A start.

Yesterday, Martinez gave up a three-run home run to Pedro Baez with two outs in the fourth after allowing a single and a walk.

“I hung a couple,” Martinez said. “I threw a couple that worked pretty good. Some of the curveballs were really good. The changeup was good. They are coming along. It just takes a little while.” Martinez, who had four strikeouts, could have gone out for another inning but his teammates forced a pitching change and he cooled down on the bench.

“It felt pretty good,” Martinez said. “I just came out here and threw the last 20 pitches — the game was taking too long — and it felt pretty good.”

Martinez said he expects to make another start in the minors before possibly joining New York. Until then, Martinez said he’s going to work on location and not results.