"Significantly disappointing," was how union president Blair Furlong described the turnout.
Atkinson told the meeting that $20,000 of the surplus, twice the previous year's amount, would be distributed back to the clubs and payments would be made by the end of next month.
"I take it that will only be to clubs represented here tonight," union life member and New Zealand Rugby Football Union director Richard Hunt quipped.
Atkinson pointed out no other union can match the Bay's record of 16 consecutive surpluses.
"It's the result of strong support from our community, the hard work Jay [union commercial manager Jay Campbell] and Dan [union sponsorship manager Dan Somerville] do, along with the good management team and good board governance."
However, Atkinson said the surplus could easily have been around the $500,000 mark had the Magpies retained the Ranfurly Shield until the end of last season. The net profit from the Magpies' only Ranfurly Shield defence, against the Counties-Manukau Steelers, was $100,000.
Delegates heard $74,128 - an increase of $62,569 on the previous year - will be transferred to the union's equity, which has increased by 9 per cent to $770, 385.
"We're getting close to the $1 million mark and I still believe this is the amount required to compete at the highest level," Atkinson said.
The union's revenue increased by $146,913 to $4,361,594 during the financial year which ended on November 30. A key factor in this increase was the New Zealand Rugby Union grants increasing by $160,731 to $1,043,038.
Revenue from season memberships dropped $21,328 to $81,845.
The union's expenses increased by $86,134 to $4,271,393. The cost of running the Magpies dropped $45,368 to $1,763,573 and Atkinson said a reduced salary cap contributed to this decrease.
Atkinson is predicting a surplus around the $20,000 mark during the $2014 financial year. However, with a Hurricanes Super Rugby match and an All Black test both scheduled for this season at McLean Park, this is a conservative estimate.
Sixty-five per cent of the union's revenue comes from commercial sponsorship and 24 per cent from the New Zealand union.
Atkinson said the national body's grants were determined by the number of games the All Blacks played and how they were performing.
Atkinson pointed out the union will spend $320,000 on the purchase of the old Napier High School Old Boys' clubrooms at McLean Park, with the aim of turning them into corporate offices for staff.
No elections were required at last night's meeting. Patron Neil Thimbleby, president Blair Furlong, Atkinson - who retired by rotation and offered himself for reappointment, as did rugby director Simon Tremain - were all re-elected unopposed.
Providing the elections are ratified at the special general meeting, the union's officers will be: patron, Neil Thimbleby; president, Blair Furlong; chairman, Brendan Mahony; directors, Kevin Atkinson, Dan Druzianic, Peter Fleming, Grant Gilbert (co-opted schools representative), Steve Lunn, Neil Pulford, Taine Randell and Simon Tremain.