Africa minister Mark Simmonds says he cannot claim enough parliamentary expenses to house his family in Westminster

A Foreign Office minister who resigned on Monday has blamed "intolerable" expenses rules for forcing him to choose between his family and his parliamentary career.

Mark Simmonds, the Africa minister, said he would stand down from government immediately and would leave his Boston and Skegness seat at next year's general election.

He said that the total allowances of £27,875 a year would not be enough to maintain a family home in Westminster and that he would not be prepared to live outside central London.

Simmonds earns £89,435 a year as an MP and minister and employs his wife Lizbeth with up to £25,000 of public money.

His reasons for stepping down have been heavily criticised on Twitter and have exposed the differences in perception of many MPs – who believe that the expenses regime is penalising their ability to live normal family lives – and voters who still believe parliamentarians receive too much public money.

His resignation comes just days after Lady Warsi resigned from her Foreign Office post over the government's policy on the crisis in Gaza.

Simmonds said he was leaving primarily so he can spend time with his family because he cannot afford to house them in central London.

"The allowances that enable members of parliament to stay in London while they are away from their families – my family lives in Lincolnshire in my constituency – does not allow me to rent a flat that could accommodate my family. So I very rarely see my family and I have to put family life first and every single parent listening to this will hopefully understand," he told the BBC.

After a spokesman for the expenses watchdog Ipsa pointed out that he has never tried to claim for a flat – he has instead claimed thousands of pounds in hotel fees – Simmonds retorted that there has not been enough support from the parliamentary authorities.

He told the Radio 4's PM programme: "It is primarily financial support that is needed … It doesn't stretch anywhere near the cost of renting a flat in Westminster.

"Of course if MPs want to get into the business of travelling extensively from Westminster to the outer reaches of London to rent a flat then that's up to them but that's not the lifestyle I want and it's not the lifestyle I have chosen for myself or I want for my family."

Last year, Simmonds was named by his local paper as the most expensive MP in Lincolnshire after it was calculated that he had claimed £173,436.96 in expenses for 2013.

Downing Street said Simmonds' resignation was unrelated to Warsi's departure. Simmonds had agreed to resign at the time of last month's reshuffle after deciding not to contest his seat at the next election. But he was allowed to stay on to chair a meeting of the UN security council on the Democratic Republic of the Congo last week. The UK assumed the presidency of the security council on 1 August.

Simmonds is the latest Tory MP to announce stepping down in a seat targeted by Ukip. Laura Sandys is standing down in Thanet South, which is expected to be contested by the Ukip leader, Nigel Farage.

Gawain Towler, a leading Farage ally, tweeted after Simmonds' announcement: "Mark Simmonds going, nothing to do with the impact of Ukip in his constituency." The prime minister praised Simmonds, but relations became strained when Simmonds missed a key vote on Syria during last year's recall of parliament because he was at a meeting to discuss Rwanda with Justine Greening, the international development secretary.

Simmonds is replaced by the highly Eurosceptic former whip James Duddridge, who said last year that Britain should tell the EU to "sod off" rather than pay benefits to Romanians and Bulgarians.

• This article was amended on 12 August 2014. An earlier version said "that the rental allowance of £27,875 a year plus £2,500 for each of his three children would not be enough to maintain a family home in Westminster". This has been corrected.