Murray Potts, who ran the site, told APNZ in an email: "The website is tainted now."
He said he decided to "pull the plug" because he obviously did not have the support of the union or the Kerikeri Rugby Club, which he had relied on for event, draw and result information.
Mr Potts stressed his website was not the official site of the club, which his son plays for in an under-11 team.
He said the website had published more than 500 rugby articles, including detailed junior rugby game summaries and photos, but none of that mattered because of "one photo of a girl in a bikini".
Mr Potts said it was wrong to have posted the photo and he had extended an apology to Ms Clare.
Ms Clare earlier said Facebook was a public forum and she was not really bothered by the photo.
Northland Rugby Union chief executive Jeremy Parkinson had described the photo and caption as "totally inappropriate" and said the union had asked for it to be taken down.
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