Today's edition of the newspaper featured the pictures despite reports earlier in the week that the feature had been dropped.
On Tuesday The Times, The Sun's sister newspaper, reported that topless models would no longer be shown on Page 3.
But The Sun today said under the headline Clarifications And Corrections: "Further to recent reports in all other media outlets, we would like to clarify that this is Page 3 and this is a picture of Nicole, 22, from Bournemouth.
"We would like to apologise on behalf of the print and broadcast journalists who have spent the last two days talking and writing about us."
The EA, representing more than two million evangelical Christians, said it was 'disappointed' the feature had returned after a 'refreshing break'.
General Director, Steve Clifford, called on members to boycott the newspaper: "Topless models in a family newspaper is not a good thing for society or the young, impressionable minds that are exposed to this bottom shelf newspaper.
"Of course, what newspapers publish is a matter for newspapers and editorial decisions are for editors, but when these decisions impact negatively on society then society needs to take a stand.
"Their editorial decisions appear to be more based on how much money they think they will make from large circulations and high advertising rates and are not in the interest of the well-being of our society.
"Perhaps the time has come for advertisers to reconsider their relationship with The Sun. Page 3 not only demeans women but it is the thin end of a very large billion-pound pornography industry.
"The Evangelical Alliance represents more than two million evangelical Christians across 79 denominations in 3,500 churches. We are also networked into scores more organisations. I am urging the membership of our constituency to stop buying the weekday edition of The Sun."
Catholic former MP Ann Widdecombe told Premier a boycott could be the only way to force The Sun to drop topless models.
"Public pressure should be applied. As long as people buy The Sun in the volume that they do buy The Sun, looking at it from the editor's point of view, why change it?" She said.
Premier's Des Busteed speaking to Chine Mbubaegbu from the EA on Premier's News Hour: