GP leaders said the compromise meant ministers had removed the worst parts of their proposals leaving a workable contract.
GPC Northern Ireland chairman Dr Tom Black said: 'Ours is a much better deal than England's, which was an example of thuggish behaviour. The deal is a significant amelioration from the original imposition.'
He warned Northern Irish practices could yet face profit drops forecast elsewhere. 'It is very difficult to tell at this stage. With the new indicators and their changes we could well see a negative number,' he added.
Agreement was reached between Northern Ireland GPC and Northern Ireland's Department of Health, Social Services and Public Safety (DHSSPS) ahead of the 1 April implementation date.
New contract detail includes no MPIG removal, an extra £3.5m funding for QOF, 13 indicator threshold increases and 83 organisation points scrapped and funding directed to the global sum equivalent.
The DHSSPS agreed to postpone any MPIG phase-out until work with Northern Ireland GPC to assess its impact was complete.
DHSSPS's original changes included axing MPIG top-ups to core funding and 23 indicator threshold changes. Under the agreement the majority of new clinical indicators recommended by NICE will be introduced except NM47 (COPD), which is deferred until 2014/15.
The threshold for CHD12 will be capped at 90%. The lower thresholds will be increased by 20% as proposed.
Dr Black said the agreement was a compromise that removed those indicators GPs felt were 'impractical or impossible'.