Wozniacki was furious that her second round match was played on an outside court while five-time major winner Sharapova was playing all of hers in Arthur Ashe Stadium.
The Danish woman said it was "unacceptable and questionable" for Sharapova, who is playing her first Grand Slam since the end of a drugs ban, to be given the showpiece court.
"With regards to scheduling, as you know, I don't make the schedule," said Sharapova after reaching the fourth round with a 7-5, 6-2 win over Sofia Kenin of the United States.
"That's not what matters to me. All that matters to me is I'm in the fourth round. Yeah, I'm not sure where she is."
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Wozniacki, who has never won a Grand Slam, lost her second-round match to Ekaterina Makarova on Wednesday after being scheduled on Court 5 before getting bumped up to Court 10.
"When you look on Center Court, I understand completely the business side of things, but someone who comes back from a drugs sentence -- performance enhancing drugs -- and all of a sudden gets to play every single match on Center Court, I think that's a questionable thing to do," fumed the Danish former world number one.
Her world ranking of 146 meant she needed a wild card to get into the main draw at the US Open.
But she has responded to the decision by the US Tennis Association by knocking out world number two Simona Halep in the first round and recovering from a set down to beat Timea Babos in the second.
On Sunday, she will face Latvian 16th seed Anatasija Sevastova for a spot in the quarter-finals.
She was broken three times and her 38 winners just offset 33 unforced errors.
"She had really nice words for me in the locker room, which was really nice," said Sharapova, older than her opponent by 12 years and regarded as an idol by Kenin.
"I wasn't surprised with the way she came out and competed. She was down I believe a few match points in the previous match.
"She's a grinder. She'll get many balls back. Despite not having the experience, she's a tough player.
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