A controversial advert on the Glasgow underground system which attacked the Scottish media has been taken down for breaching political neutrality rules.

Strathclyde Passenger Transport said the advert for the Wings over Scotland website contravened its rules forbidding ads of a political nature and, on Tuesday night, ordered them to be removed by its advertising contractor Primesight.

The site, run from Bath by blogger Stuart Campbell, had bought 41 subway carriage poster sites for an ad claiming there were 37 "national or daily" newspapers in Scotland, with only five Scottish-owned and none of them supporting independence.

Its concluding line read: "Wouldn't you at least like to hear both sides of the story?"

In a statement, SPT, a publicly-owned transport authority, said: "SPT advertising contract guidelines state that Subway sites should not be used to campaign or lobby for political benefit.

"Our advertising agency applies that standard to all commercial bookings but unfortunately this particular ad slipped through their net. The ad was taken down as a result."

Campbell told the Guardian that he had not been warned by Primesight that adverts of a political nature would be banned.

But Primesight stated on Wednesday that Campbell had twice described himself as a charity when he signed the original contract with them, which meant the advert sidestepped its normal political screening.

"The contract went to the client to agree the booking via Echosign, our online portal for contracts," the firm said in a statement.

"The business was listed as a charity in both campaign description and trade category entries. As such we accepted the booking.

"If this had said political then we would have been unable to book on our system due to the prohibition."

Campbell said that Primesight had designated him as a charity, and he had sought to clarify his status after signing the contract.

"The thing that came through listed us as that, through no choice of mine," he said.

He said he had emailed them to say: "NB In case it's important for anything, we're not actually a 'charity'. I don't know what the heck we are, to tell you the truth."

He received an email back from Primesight saying: "That's OK and not a problem. Will you be available for me to call you to arrange payment for this?"

The ad, which had been put up in a handful of carriages before the ban was imposed on Wednesday evening, was attacked by newspaper journalists on Twitter for implying the press was biased and was censoring the pro-independence case, but vigorously defended by the website's followers.

As its fans accused SPT of political censorship, Kenny Farquharson, deputy editor of the Scotsman and Scotland on Sunday, challenged Campbell to justify the figures and definitions he used in the advert on Twitter.

SPT confirmed it had been received complaints from Campbell's readers, some alleging bias because the free newspaper Metro, which has a distribution contract to be given away on the subway, carried an anti-independence advert.

Campbell said: "The advert made no political statements whatsoever.

"The website is of course political, but no more so than all the newspapers the subway is happy to promote – including the Metro, owned by the virulently and openly union-supporting Daily Mail, which is distributed on subway property and ran a full-page anti-independence ad in highly intemperate language the morning after our posters were pulled. Clearly the ban only applies to one side of the independence debate."

Campbell has told his followers he has raised more than £100,000 from crowd-sourcing websites for the blog, to fund a salary, pay the site's running costs and pay for opinion polling. He confirmed he used that cash to pay the fee for the subway ads.

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