The contract agreement that the New York Philharmonic reached with its musicians last week will keep the music playing at Avery Fisher Hall and spare the city from the kind of bitter labor unrest that has set off damaging strikes and lockouts at other orchestras.

But it leaves both the players and management facing real challenges.

While the deal calls for the musicians to receive modest raises — which will increase their salaries by 6.5 percent over the next four years — those raises will not be big enough for them to reclaim the status they once held as the nation’s highest-paid symphony orchestra musicians. In a blow that is both psychological and economic, base pay at the Philharmonic, which is the oldest symphony orchestra in the nation and one of the most prestigious, has in recent years fallen behind that of orchestras in Los Angeles, Chicago, San Francisco and Boston.

And though the Philharmonic’s management won some concessions — the players agreed to begin contributing to their health-care coverage in 2015 — the agreement will do little to significantly cut the mounting costs that have left the orchestra with growing deficits. The deficit reached $6.1 million in the 2012-13 season, on a budget of $71 million.

Both sides expressed relief that an amicable resolution had been achieved during what has been a difficult time for orchestras. Labor strife has left the Minnesota Orchestra locked out of its hall for more than a year after its players rejected proposals that would substantially cut their pay. That dispute cost the ensemble its respected music director, Osmo Vanska, who resigned after the lockout forced the cancellation of the orchestra’s concerts this fall at Carnegie Hall.