The pandemic has led to a sharp fall in the number of children around the world being vaccinated, the UN says.
The decline in immunisation against diphtheria, tetanus and whooping cough over the first four months of the year is the first in nearly three decades.
World Health Organization head Dr Tedros Ghebreyesus said vaccines were a hugely powerful public health tool.
He said the suffering and death caused by children missing out on vaccines could dwarf that caused by the virus.
Immunisation programmes in three-quarters of the more than 80 countries that responded to a UN survey have been disrupted, Unicef and the WHO said.
They said the disruptions were linked to a lack of personal protective equipment for health workers, travel restrictions, low health worker staffing levels and a reluctance to leave home, all of which saw programmes curbed or shut down.
By May this year at least 30 measles vaccinations campaigns had been cancelled or were at risk.
Measles outbreaks were already rising before the pandemic struck, with 10 million people infected in 2018 and 140,000 deaths, most of whom were children, according to UN data.
Unicef head Henriette Fore said the coronavirus had made routine vaccinations a "daunting challenge".
"We must prevent a further deterioration in vaccine coverage... before children's lives are threatened by other diseases, she said, adding: "We cannot trade one health crisis for another."
Disruption to the global immunisation programme is extremely bad news, particularly for the world's poorest countries. It is estimated that immunisations save up to 3m lives a year by protecting children against serious diseases.
The Unicef programme is specifically targeted at children who would otherwise struggle to receive good quality health care, but although vaccines now protect more children than ever before, millions of children still go without protection, and it is estimated that more than 1.5m people die each year from diseases that vaccines could prevent.
Experts believe that low immunisation rates among poor and marginalised children seriously compromise all the gains made in other areas of maternal and child health, so major disruption on the scale outlined in this new report will inevitably cost a lot of lives.
Coronavirus has consumed huge amounts of healthcare resources worldwide as the international community has focused on efforts to combat the deadly impact of the virus.
It has also made delivery of healthcare difficult, particularly in poorer countries where supply chains have been disrupted, facilities and protective equipment can be basic, and fear of being infected has put people off attending clinics. But diseases such as measles, diphtheria, and cholera are already on the rise, underlining the urgency of finding ways to tackle this problem.
Progress on immunisation had already been stalling before the pandemic, the UN agencies said.
In 2019 nearly 14m children - more than half of them in Africa - did not get life-saving vaccines against diseases such as measles and diphtheria. Two-thirds of them were in 10 countries: Angola, Brazil, DR Congo, Ethiopia, India, Indonesia, Mexico, Nigeria, Pakistan, and The Philippines.
Meanwhile, historically high rates of immunisation had fallen in Latin America and the Caribbean, the UN said, with immunisation coverage falling by at least 14 percentage points in Brazil, Bolivia, Haiti and Venezuela over the past decade.
"The likelihood that a child born today will be fully vaccinated with all the globally recommended vaccines by the time she reaches the age of five is less than 20 percent," Unicef and the WHO said.