It has identified two locations between Junction 10 at Burnley and Junction 14 at Boundary Mill where heavy rain can lead to flooding on the motorway.
The council said upgrades to prevent future flooding incidents will require “significant” funding.
It comes after complaints about standing water on the highway following recent heavy rainfall, which poses a risk to road users.
Until funding becomes available, an LCC spokesperson said it will “continue responding” to any flooding reports, adding that it “regularly clears” the drainage around these areas.
At a Pendle Council meeting, councillors said they will write to Lancashire County Council to take “urgent” action to prevent further flooding.
A spokesman for Lancashire County Council said: “We maintain a section of the M65 between Junction 10 at Burnley and Junction 14 at Boundary Mill, and we regularly clear the drainage to help reduce the risk of flooding.
“Through our investigations, we’ve identified two locations where heavy rain can cause localised flooding, and improving these sites will require significant investment.
“Until funding is available, we will continue to respond to any flooding reports, working closely with the police to keep road users safe.”
Parts of the M65 have flooded in the past, including on December 10, when flooding forced traffic to a standstill around junction 13.
Previous disruption has also been reported at junction nine in Hapton.
Contractor Balfour Beatty, which has successfully delivered major motorway schemes across the North West, will start work on site in January.
In anticipation of the work starting, site compounds are being set up next to the junction off Belthorn Road and at Blackburn with Darwen Council’s Davyfield depot.
Once work begins, the main construction will take place during off-peak times, between 9.30am and 3.30pm, to help keep disruption to a minimum.
Emergency services, including representatives from Royal Blackburn Hospital, have been involved in the planning, and the scheme will be under constant review by National Highways to monitor any impact on congestion.
A spokesperson for Pendle Council said: “At Pendle Borough Council’s full council meeting on Thursday, December 18, councillors resolved to write to Lancashire County Council requesting that they take urgent, effective action to prevent flooding on the M65.
“This decision was made after consideration of a motion on serious safety concerns arising from continuing and persistent flooding on the M65.
“A letter in these terms is currently being prepared to be sent to the county council.”