Kohli slipped two places to be placed eighth, followed by Raina at ninth. Yuvraj Singh was at 14th after a fall of one place while Gautam Gambhir was down at 17th.
In the T20 bowling chart, Ravichandran Ashwin, the only Indian in the list, slipped two places to be positioned 18th.
In the all-rounder's list, Yuvraj Singh retained the third position with 337 points.
In the team rankings for ODI, topper India have 119 points, followed by England and Australia.
England have an opportunity to reclaim the number-one ranking on the ODI Championship table when they take on New Zealand in a three-match series that commences in Hamilton from Sunday.
England are on equal points with India (119 ratings points) but are ranked behind the world champions as ratings are calculated beyond the decimal point.
If England win all three matches, they will reclaim the number-one ranking.
In the T20 rankings, England's Alex Hales and Steven Finn, along with West Indies' Sunil Narine, have achieved career-best rankings in the latest list.
The latest rankings were released at the completion of England's 2-1 series win over hosts New Zealand yesterday and West Indies' win over Australia in the one-off match.
While Hales has jumped nine places to a career-best fifth in the rankings for T20I batsmen, Sunil Narine has leaped six places to a best-ever third and Steven Finn has moved up 20 places to a career-best sixth in the rankings for T20 bowlers.
Also making an upward movement within the top 10 batters is New Zealand's Martin Guptill, who has moved up five places, to join former Sri Lanka captain Mahela Jayawardene in third place.