Matt Harvey continued to be the weakest link in the Mets’ rotation on Tuesday night. Feeling under the weather and pitching in poor weather, Harvey allowed three runs in 5 2⁄3 innings to the anemic Braves and the Mets were one-hit by Matt Wisler and Arodys Vizcaino in a 3-0 loss before 27,356 at soggy Citi Field.

Harvey (2-4, 4.76 ERA) was sick on Monday, according to manager Terry Collins. But the Dark Knight had improved enough to face the Braves, who came in with a 6-19 record, including defeats in all four previous games with the Mets.

Atlanta had hit five home runs on the season, or four fewer than Mets second baseman Neil Walker. But Harvey gave up a fifth-inning home run to Mallex Smith to snap a scoreless tie and allowed two more runs before getting knocked out in the sixth.

The middle innings continue to be a problem for Harvey. Collins even suggested Harvey could be paying now for all of the innings he threw last season in his first year back from Tommy John surgery.

“As it starts to get a little warmer, maybe we can kind of make a determination if the arm strength’s going to come back,” Collins said. “Or if it’s going to be one of those years where he’s just going to due to all the innings last year we’re going to see the effects of it.”

Harvey said he didn’t think Monday’s illness or last season’s workload are to blame. He also said he has many questions and few answers about his struggles.

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“I think there’s just a lot of things going on,” he said. “Right now, I’m not feeling good with my mechanics, not feeling good throwing the ball. It’s frustrating. I think I’ve said it before: I’m the one who’s most frustrated here about what’s going on. It’s been a frustrating start, but we have a long way to go.”

Harvey allowed eight hits, walked two, struck out four and threw two wild pitches — including one that allowed a run to score — in a 100-pitch effort.

On the offensive side, the Mets’ homer-happy bats were stifled by Wisler, who didn’t allow a hit until Asdrubal Cabrera singled to center with one out in the fifth. The Mets hit several balls hard but got almost nothing to show for it.

“I thought we hit some balls pretty good,” Collins said. “But that’s part of the game. Once in a while, people are standing in the right spots.”

Wisler (1-2, 3.24) went eight innings. The righthander walked two, hit a batter and struck out four. In his brief career, the 23-year-old Wisler is 3-1 with a 1.55 ERA against the Mets and 6-9, 5.08 against the rest of baseball.

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The Mets had won nine of 10 — beginning with a three-game sweep in Atlanta on April 22-24 — and had hit 34 home runs in their last 16 games. Since hitting three home runs and scoring four runs in the first inning Monday, the Mets have been shut out for 17 straight innings.

But it was the Braves who got on the board first in the fifth when Smith hit an opposite-field shot into the leftfield corner that was just fair and just over the orange home-run line.

Smith’s ball was originally ruled in play and went for an apparent triple as the ball caromed past Michael Conforto. But the umpires huddled and crew chief Gary Cederstrom called for a replay review. It took only 50 seconds to award Smith the first home run of his career.

In the sixth, A.J. Pierzynski had an RBI double. The Braves’ third run scored on a wild pitch.