Malcolm Turnbull's Small Business Minister has charged taxpayers nearly $50,000 to stay in his wife's Canberra apartment but has defended the spending by comparing his travel allowance to penalty rates.

Michael McCormack is one of about 50 federal politicians believed to use their $273-a-night Canberra travel allowance to help pay off a second home. His wife bought the property in the leafy suburb of Kingston - close to Parliament House - in May 2013 and he now stays there whenever he visits.

The Nationals MP claimed $48,256 in Canberra travel allowance between May 2013 and June 2016 and has likely claimed close to a further $10,000 in the last nine months, although those expenses have not yet been disclosed.

The allowance comes on top of his ministerial salary of $313,500.