His record after four games was 2-1 with a 2.59 ERA.
But over his last three starts, the 25-year-old former independent league starter has surrendered 15 runs on 19 hits and five walks in just 13 1/3 innings. On Friday, the San Francisco Giants scored three runs off Werner on eight hits in 4 2/3 innings en route to a 3-1 victory.
The eight hits included two line-drive doubles and two triples.
Padres manager Bud Black said Werner's problems could be growing pains.
"He's learning," Black said. "We've seen some good work from Andrew this season. The Giants tonight were more selective. They drove up his pitch count. His stuff was fine. The Giants just had a plan against him."
Werner is one of several young Padres on the bubble to retain their spots on the 40-man roster.
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