The government had put curbs on the media on Saturday and lifted the ban on Tuesday, saying the decision taken at some "local" level was a mistake.
But newspapers refused print runs, alleging that the authorities were denying that the government had banned newspaper publications in the valley.
The logjam was resolved in a meeting on Wednesday between Chief Minister Mehbooba Mufti and editors of Srinagar-based newspapers.
Editors and publishers said the Chief Minister "regretted" the ban and assured them of unhindered news gathering, printing and distribution.
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