Chief Executive Neil Bausor explained that the extended reporting period, which has been adopted across the group of which the club forms part, was introduced to bring the club's financial year into line with the football season.
"With player wages being the club's largest overhead and contracts running on an annual basis to June 30, it makes sense for the financial year to reflect the football year," he said.
The accounts show the challenges of managing budgets in football clubs following relegation from the Premier League. Even with parachute payments, albeit at reduced levels, the club has required continued support from its parent company.
"Our parent company has backed Middlesbrough Football Club at the level of approximately £1m per month for this reporting period and this is in addition to substantial investment in previous years," continued Mr Bausor.
The Football League is currently working on introducing new financial fair play rules in the Championship and this will cap the allowable financial support that clubs are able to receive.
The parent company has agreed that it will continue to support the club up to the maximum levels possible under the currently proposed new rules in order to maximise the club's opportunity to return to the Premier League.
A note to the accounts explains that the club is now free from debt owed to external providers, and this is due to the support of the parent company.
"The continued support of our dedicated fans, alongside the ongoing support of our parent company, is crucial to the success of the team," said Mr Bausor. "In the absence of Premier League TV money, the main income stream for Championship clubs is gate receipts."