Armed rebels from the Mai-Mai militia attacked Katwa hospital near the city of Butembo at around 3.40 am (0140 GMT), officers told AFP.
“We have resisted and repelled the attack even though these ‘Mai-Mai’ had a PKM machine gun,” said Butembo police chief Colonel Paul Ngoma.
He said one rebel was killed and four captured.
The attack came a day after a WHO doctor, Richard Valery Mouzoko Kiboung, was shot dead in an assault by armed militiamen on Butembo University Hospital, according to the World Health Organization.
The WHO said the epidemiologist had been deployed to help combat Ebola in the region.
The attacks are the latest in a string of assaults on teams grappling with a near nine-month-old Ebola outbreak that has claimed almost 850 lives.
UN Secretary General Antonio Guterres on Friday condemned the Butembo University Hospital attack and called on Congolese authorities to bring the perpetrators to justice.
DR Congo declared its tenth outbreak of Ebola last August, in northeastern North Kivu province, before the virus spread into the neighbouring Ituri region.
Local organisations have said the number of Ebola deaths is rising.
An updated toll by the health ministry, issued on Wednesday, said there had been 843 deaths since August.
WHO data from April 9 put the number of confirmed or probable cases at 1,186, of which 751 had been fatal.
The outbreak is the second deadliest on record, after the epidemic that struck West Africa in 2014-16, which killed more than 11,300 people.
Efforts to roll back the highly contagious haemorrhagic fever in DRC have been hampered by fighting but also by resistance within communities to preventative measures, care facilities and safe burials.
On March 9, an attack on a treatment centre at Butembo left a policeman dead and a health worker wounded. It was the third attack on that centre.
On February 24, a treatment centre in Katwa was set ablaze.