The four acrylic canvas works by local artist Joe Greenwood were on display at Portsmouth's Anglican cathedral as part of a summer show by the Portsmouth and Hampshire Art Society (PHAS).
But a cathedral spokesman said that a number of visitors complained about the paintings, leading to the decision to remove them.
The Diocese of Portsmouth spokesman said: "Portsmouth Cathedral aims to be a space open to everybody.
"Whenever a public exhibition takes place in a church it is important to weigh up how it relates to our main purpose of being a place for prayer, reflection and worship.
"When planning the exhibition the paintings were considered to be suitable but a number of visitors and regular worshippers expressed distress about them and, in consultation with PHAS, it was decided to remove them from the exhibition.
"This decision is not a reflection on the quality of the artist's work but on our duty to balance the needs of all those who come to the cathedral."
Mr Greenwood, 40, from Southsea, told the Portsmouth News: "This was my first proper exhibition, so it makes me sad my paintings have been misconstrued in this way.
"Nudity itself is not a sexual thing, it's just a human form, and there is a lot of it in religious art - look at the Sistine Chapel for example."
Paul Buckley, PHAS chairman, said: "The terms of the hire agreement with Portsmouth Cathedral are that they reserve the right to consider some material unsuitable for display in a cathedral.
"We do warn participating artists about the venue and suitability of submissions.
"When these paintings were presented we discussed them with the cathedral clergy and received permission to hang them on panels well away from and screened from the altar.
"Unfortunately during the first few days of the exhibition it appears there have been complaints and objections from members of the cathedral congregation, which we have not seen.
"The cathedral has therefore asked us to withdraw them and within the terms of our agreement we have done so.
"This is unfortunate for the artist but we must respect the cathedral."
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