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.

Having started their campaign with a 2-0 win over Hungary on Wednesday, Wales had chances to score in the first half through Natasha Harding and Rachel Rowe.
Both teams came close to scoring after the interval, with Rowe's overhead kick going wide.
Wales face Republic of Ireland on Monday, 6 March, with a finals day on Wednesday, 8 March.
Wales Women's Squad: Claire Skinner (Cyncoed), Laura O'Sullivan (Cardiff City Ladies), Emma Gibbon (Eastern Suburbs FC), Loren Dykes (Bristol City Women), Hannah Miles (Cardiff City Ladies), Hayley Ladd (Bristol City Women), Sophie Ingle (Liverpool), Gemma Evans (Cardiff City Ladies), Shaunna Jenkins (Cardiff City Ladies), Jess Fishlock (Seattle Reign FC - on loan at Melbourne City), Angharad James (Notts County Ladies), Charlie Estcourt (Reading FC Women), Bronwen Thomas (Brighton & Hove Albion Women), Georgia Evans (Bristol City Women), Nadia Lawrence (Yeovil Town Ladies), Helen Ward (Yeovil Town Ladies), Natasha Harding (Liverpool), Rachel Rowe (Reading FC Women), Kayleigh Green (Chieti), Melissa Fletcher (Reading FC Women), Rhiannon Roberts (Doncaster Rovers Belles), Amina Vine (Bristol City Women), Emma Beynon (Swansea City Ladies).
Residents whose homes have been filled with hundreds of flies from a Derbyshire recycling site have been told their misery is over.
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Wales Women drew with Czech Republic in their second game of the Cyprus Cup.