Fly swarms from the Shows Waste Management site in Slack Lane, Derby, have left residents facing difficulties cooking and cleaning for weeks.
The Environment Agency said 2,200 tonnes of waste has now been moved and "the fly issue...has been resolved".
The site has been ordered by the agency to move all waste by 7 July.
The agency had started a criminal probe into the fly infestation, and a spokesman added they would "seek to take the appropriate level of enforcement action against relevant parties" once their investigation into the cause of the plague is over.
"We can confirm that the fly issue on the site has been resolved with no reported issues from the community since early June," an agency spokesman said.
"We will continue to monitor and assess the situation until our requirements have been fully met."
About 3,000 households and businesses are in the affected areas.
One resident, Melissa Marriott, previously told the BBC she has been unable to have a bath without flies getting into the water, and had to resort to buying an electric fly killer which "gets 50 flies a day".
Another resident, Jenny Warren, said the flies had been "all over the food and you can't open windows".
On 17 May, Shows Waste Management was given a suspension order by the agency and told no further waste would be accepted on site.
The waste company has said it was in the current situation because of a dispute with another firm.
Residents whose homes have been filled with hundreds of flies from a Derbyshire recycling site have been told their misery is over.