The funding would be cut by 3.6%, or about $198,000, Clutha Community Health Company chairman Brian Dodds said.
Originally, SDHB had proposed a 5% reduction of $273,860, he said.
Clutha Health First agreed to a five-year contract with the government-funded organisation.
A separate agreement was reached for Clutha Health First to continue a $75,000 contract to assess patients' needs in the district, Mr Dodds said.
He described the the funding cut as ''uncomfortable'' but said it was important to ''try to control our own destiny, get an agreement while the opportunity was there that we could live with''.
''We can't be immune from the challenges that the district health board is facing.
''To expect that there won't be some adjustment on funding is too much to hope for.''
Last week, Health Minister Jonathan Coleman told the SDHB it needed to explain why a commissioner should not be appointed to replace its board.
The board has been scrutinised over the unpopular round of cuts it proposed in the face of a projected $42 million financial year deficit.
Clutha Health First chief executive Ray Anton said the possibility of the SDHB board's replacement by a commissioner had not influenced his board's decision.
''We did not know about the commissioner until everybody else. Our negotiations were leaning towards a resolution earlier than that.''
The loss of revenue would not result in a reduction in service levels or staffing, Mr Anton said.
Although the company was in a good financial position, surpluses Clutha Health First had enjoyed would ''likely disappear''.
''We've had good revenue sources from our other income sources.''
The company had revenue options by providing GP, ACC and corporate services.
''As a business, we're finding other ways of generating income that help us diversify away from the DHB,'' Mr Anton said.
The SDHB had assured Clutha Health First its outpatient clinics were not under threat, nor was the revenue from the number of in-patient beds, and X-rays the SDHB bought from Clutha Health First.
Further, Clutha Health First had a commitment from the SDHB to pass on all future allowances for increased costs that were passed on from the ministry.
Mr Anton said Clutha Health First was in ''good shape'' and the longer term for the contract would provide stability.
''We've negotiated a five-year contract with future cost increases built in and maintained a range of services that are important for this region, and we believe that is a secure contract for the five-year period.
''Hopefully, that will take us through the choppy water the DHB is going through right now.''
Mr Anton said he was writing a budget that would go to his board shortly, reflecting the loss of revenue and projecting the next 12 months.
Yesterday, Central Otago Health Services Ltd chairman Russell McGeorge said he was not ready to announce anything about the progress of COHSL's funding contract. COHSL runs Dunstan Hospital at Clyde.
The SDHB did not reply to requests for comment late yesterday.
Clutha Health First
• Began operating December 1998.
• Accepted a 3.6% funding cut from SDHB.
• 2014 income rose more than $8.6 million, up more than 10% on previous year.
• GPs accounted for 55.4% of 2014 increase.
• The general practice had 34,869 patients attending in 2014.
