The SNP minister had been under pressure after reports of the huge bill surfaced on Wednesday evening.
Mr Matheson had initially agreed to contribute £3,000 from his own office expense allowance to the £10,936 bill, with the rest of the cost being met by the Scottish Parliament. Both payments would have come from the public purse, rather than his own pocket.
“I have contacted the Scottish Parliament authorities this afternoon to make arrangements to reimburse the full cost of the £10,935.74 incurred in roaming charges on my parliament iPad,” he said.
“While the Parliament agreed to pay the bulk of this sum as a legitimate expense, with the rest being met from my office allowance, I have reflected long and hard and accept that the SIM card on this device should have been replaced at an earlier stage.
“Much of the speculation in the past couple of days has questioned my integrity, and I take this extremely seriously. I take equally seriously the reputation of the Scottish Parliament, of which I have always striven to be a diligent member since its restoration in 1999.
“It is my decision to reimburse these costs in full, which I believe in all the circumstances to be the right one.
“As well as being a constituency MSP, I have an important role as Health Secretary and the coming months will be challenging for our health service. I am determined to be fully focused on taking forward these responsibilities, and I assure the people of Falkirk West and across Scotland that their concerns are my priorities.”
Mr Matheson incurred a huge fee during his week-long visit to Morocco after Christmas last year and into the New Year.
He has already told journalists that the bill was brought about by using “an outdated Sim card in an iPad that I had for constituency purposes”.
An investigation by the parliamentary authorities found that Mr Matheson had failed to update his iPad’s sim card as required, or to notify the IT office before travelling so that the appropriate roaming package could be applied. This was also required under Holyrood rules.
His political opponents called on him to foot the bill himself, after it emerged the Scottish Parliament is to carry out a policy review that will consider if MSPs should be held “personally liable for costs where they have not acted in full accordance with IT office requirements”.
Questions remain for the Scottish parliamentary authorities as to why they agreed in the first place to pay Mr Matheson’s bill when they had found that he had breached their rules.
The Scottish Conservative chairman, Craig Hoy, has written to the presiding officer, Alison Johnstone, requesting a full investigation into why and how the Scottish parliament agreed to pay the health secretary’s bill.
He also asked why the First Minister told the BBC yesterday Mr Matheson shouldn’t have to pay any money from his own pocket.
Pressed yesterday if Mr Matheson should pay the bill at his own cost, First Minister Humza Yousaf said: “No, the parliamentary authorities have already confirmed of course that it was a legitimate parliamentary expense.”
Mr Hoy said tonight: “Michael Matheson has belatedly been shamed into repaying a bill that he had the audacity to expect the taxpayer to foot.
“His arrogance and contempt for the public purse was clear from his refusal to follow parliament guidelines and inform IT staff that he was travelling abroad.
“This is not the end of the matter. Michael Matheson has to address the many serious unanswered questions over this scandal – having notably refused to do so when confronted by journalists on Thursday.
“We still need to hear a personal statement from the health secretary in Parliament and I call on him to publish the original roaming charges statement from the network provider.”
Mr Hoy added: “This also calls into question the judgment of Humza Yousaf who, just 24 hours ago, claimed that this was a legitimate expenses claim and that his health secretary shouldn’t repay a penny.”
Responding to Mr Matheson’s statement tonight, a Scottish Parliament spokesman said:
“As previously stated, Mr Matheson provided written assurance that the costs were in connection with parliamentary business.
“Mr Matheson notified the Parliament this afternoon that he would, on reflection, meet the cost of his data charges. The money will be returned to the Parliament’s budget.”