Wakefield District Housing (WDH) chief Andy Wallhead saw his earnings increase from £207,000 to £225,000 during the last financial year, trade publication Housing Today revealed last week.
The publication said the rise, of 8.7 per cent, was the third biggest of any housing association chief across the UK during that time.
Meanwhile WDH's staff were given a lump sum increase of £350 each last January, plus a £300 bonus and an extra 2.5 days "discretionary" annual leave.
Unions had asked for more, but WDH wrote to staff saying it couldn't offer anything beyond that.
Rents for social housing tenants have also risen this year, with a 1.5 per cent increase applied to a number of properties.
However, WDH said the reported £225,000 figure reflects "pay and other benefits" for Mr Wallhead, and that his actual salary had only increased by £350, to £207,350.
They also said Mr Wallhead "chooses not to accept the full salary for the role".
When asked exactly how much he does accept however, WDH said this was "personal information" and could not be revealed.
A spokesperson for the organisation said: "The level of remuneration offered to WDH’s management team is independently scrutinised and benchmarked and approved by WDH’s board.
"Salaries are set at the median level for similar roles across the sector.
"The figures published by Housing Today showed information on the chief executive’s earnings including pay and other benefits, the figures do not reflect the salary for the role."
Explaining the pay increase for staff, WDH said: "The decision to pay a lump sum in place of a percentage increase, was made in order to reduce the widening gap between employees, with those earning the least seeing the biggest benefit."
In a January letter to staff, which has been seen by the Local Democracy Reporting Service (LDRS), Mr Wallhead said: "We do not feel it would be right for us to award ourselves a higher pay rise in a year when we have increased rents for tenants, who are likely to be the hardest hit by any economic challenges resulting from Covid-19.
"I believe that our pay offer is fair and more than equitable compared to other similar organisations and the circumstances we face.
"Our approach to this, and other financial matters, is to ensure that we are prudent so that our business remains strong and we are able to protect jobs and the core terms and conditions that we all enjoy."
WDH also confirmed that its executive team's total earnings rose by five per cent to £830,000 in 2020/21.
The total earnings of its board members rose by 72 per cent, to £87,280.
Explaining this, the organisation said: "With regards to the executive team, new appointments were made to meet the needs of the business.
"Executive directors received the same £350 pay award as all employees.
"To ensure we have a board that is able to provide good governance, we have increased the number of members, bringing the skills our organisation needs.
"This had a direct impact on board costs, that have been reported.
"An independent review was also carried out in 2020, which demonstrated that board members were not being paid at the median level for other board members in the sector.
"A decision was subsequently made to increase board remuneration to be consistent in our approach and ensure we continue to attract high quality members, who can provide the right skills, knowledge and expertise to act in the best interests of our tenants and employees."
WDH operates around 32,000 properties in the local area. It was set up in the mid 2000s and took over all of the existing social housing stock in the district, which had previously been run by Wakefield Council.
Local Democracy Reporting Service