Manipur went ahead as early as the 14th minute when Khantang Paite was fouled inside the Sikkim penalty area.
Paite pulled himself up and scored from the resulting penalty.
Manipur increased the lead four minutes before half-time when Subhash Singh scored.
The former champions did not allow Sikkim to make much inroads in the second half and duly won the match 2-0 .
Maharashtra also went through to the last 18 stage after defeating Meghalaya 3-0 in a Cluster II match at Coimbatore.
Maharashtra were the better of the two sides in the match but couldn't score in the first 45 minutes.
They did score eventually four minutes after the hour-mark when Paresh Shivalkar scored.
Three minutes later Maharashtra doubled their lead when Sampat Kumar Kuttymani hit the Meghalaya net.
The 3-0 scoreline was complete two minutes later when Kuttymani scored his brace.
Goa trounced Orissa 4-0 in a Cluster IV clash to book their place in the pre-quarterfinals of the 63rd National Football Championship.
Goa took the lead through Marcus Mascarenhas and stretched their lead in the 33rd minute when Beevan D'Mello scored.
It became 3-0 to Goa a minute before the half-time whistle was blown when Dempo star Climax Lawrence scored.
Goa continued to dominate the match in the second half too and made it 4-0 in the 70th minute when Riston Rodriguez scored.
In another match of the day, Haryana defeated Bihar 3-0 in Cluster VII at Chennai to book their place in the pre-quarterfinals of the Santosh Trophy.
They scored eight minutes into the match through Surender Kumar.
It became 2-0 to Bihar in the 42nd minute when Pradeep Kumar scored and the 3-0 scoreline was accomplished in the dying minutes of the game when Kumar scored his brace.