The Ebola outbreak in eastern Congo is now the world's second-biggest ever with 426 cases, according to the country's health ministry.
On Wednesday health workers launched a door-to-door, four-day blitz to control malaria in the Democratic Republic of Congo with the aim of cutting suspected Ebola cases in half.
The town of Beni in North Kivu province, currently battling the worst Ebola outbreak in Congo's history, has also seen an eight-fold increase in malaria cases since last year.
Children who went to health centers for malaria are believed to have contracted Ebola there, and about half of the people screened in Ebola centers only had malaria, said the WHO.
If malaria is reduced, health workers will be able to focus on real Ebola patients and keep others away from the wards.
Ebola has killed 240 people and infected more than 400 since July in an outbreak that shows little sign of abating.
It is spread through contact with bodily fluids and symptoms include vomiting, bleeding, and diarrhoea.
The world's worst outbreak - from 2014 to 2016 - killed more than 11,000 people in Liberia, Guinea, and Sierra Leone.
Congo is the second worst country in the world for malaria, trailing only Nigeria, and Hoyer said there were no more mosquito-blocking bed nets left in North Kivu, an eastern province that is battling both conflict and disease.
Malaria can normally be diagnosed with a rapid blood test, but the risk of Ebola transmission means health workers have to rely on an assessment of symptoms, he said.
This normally results in an over-reported number of cases - but not up to eight-fold, which is 2,000 cases a week, he said.
Starting on Wednesday, health workers planned to go door-to-door for four days in the town of Beni, delivering mosquito nets and anti-malarial drugs to 450,000 people, said the WHO.
The aim - to treat people who already have malaria and prevent transmission among others in the short-term, freeing up resources to focus on the more serious disease, it said.
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