Children receiving the first dose of the measles, mumps and rubella (MMR) has dropped from 91.2% to 90.3% - continuing a five-year downward trend.
Some 86.4% of children received their second dose of the MMR vaccine by their fifth birthday, a decrease from 87.2% in the previous year.
Children receiving first dose of MMR jab in 2018-19
Children receiving first dose of MMR jab in 2017-18
The proportion of children vaccinated against diphtheria, tetanus and polio fell to 92.1% by age 12 months - its lowest level since 2008-09 and below the 95% target.
Professor Stephen Powis, national medical director of NHS England, said: “Vaccines are a vital, life-saving part of our country’s public health and the numbers of children not being vaccinated is concerning.
“No-one should be complacent about getting their own or their child’s jabs and so the NHS is taking action, with its partners, to combat the decline and to reverse the dangerous effects of complacency about vaccines.”
The proportion of children vaccinated against rotavirus also fell, as did coverage for the pneumococcal conjugate vaccine (PCV), the combined Hib/meningitis C vaccine and the meningitis B vaccine.
Health Secretary Matt Hancock has said he will not “rule out” bold action to protect children, if vaccination rates fail to improve.
Mr Hancock, who said in April he could not rule out the possibility that unvaccinated children would be sent home from school in future, warned that “devastating diseases can, and will, resurface”.
The Department of Health and Social Care said a range of options have been suggested, including mandatory vaccination.
Mr Hancock said: “Falling childhood vaccination rates are unacceptable. Everyone has a role to play in halting this decline.
“The loss of our measles-free status is a stark reminder that devastating diseases can, and will, resurface.
“We need to be bold and I will not rule out action so that every child is properly protected.”
Dr Mary Ramsay, head of immunisation at Public Health England (PHE), said even thought the changes are small proportions, they are "big drops in terms of public health."
She added: “The trend is a concerning continuation of what we’ve seen in the last five years.
“No parent should be in any doubt of the devastating impact of these diseases.
“It’s vital that everyone recognises the value of vaccines and takes up this life-saving offer.”
Professor Helen Stokes-Lampard, chairwoman of the Royal College of GPs, said: "Even a small drop in the take-up of vaccinations is disheartening and very concerning.
"We are aware of the destructive anti-vaccination messages that are circulating online and via social media, and these are perpetuating toxic myths that are not backed by any evidence or false claims that have been completely debunked.
"Parents need to be aware of the clear, evidence-based findings about the safety and effectiveness of vaccines.
"It is also important for people to understand that the decision to vaccinate their child doesn't just affect them, but society as a whole, and that it would be incredibly dangerous if we were to lose the protection of herd immunisation against a host of serious, and potentially deadly, diseases."
Jo Walton is living the painful consequences of not vaccinating her daughter Sarah.
"The impact is devastating. it's like being stuck in a prison," Jo said.
Sarah got measles as a baby just as she was about to get her vaccination.
A later measles infection as an adult left her severely disabled from a life-changing brain condition.
Jo told ITV News: "I'm finding it difficult to understand why parents are choosing not to vaccinate, or not making sure that they vaccinate and choosing instead what may result in what's happened to Sarah."
Dr Andrew Parson, chair of NHS Bromley Commissioning Group, have previously written to the Health Secretary to make the MMR jabs compulsory.
He says this decline is a "worrying trend", and believes it is mostly led by the fact people don't remember what the deadly ramifications in the days before vaccination.
"We could be facing an epidemic in the future of a preventable disease that potentially could seriously lead to children dying," he said.
He said it was important the NHS makes "all of the scheduled vaccinations really visible and the parents are aware they've got the right literature."
He adds that in places like London where people tend to move areas a lot more, it's incumbent on GPs to keep track of this, and provide "catch up" opportunities for children who have missed vaccinations.
Some mothers say doctors don't often give enough information on why the vaccines are important, and the ramifications of missing a jab.
With one mum, she told ITV News she received a leaflet from her doctor with all the information on vaccines and when she should get her daughter vaccinated.
However, for her eldest son, she says she was left to remember the appointments for herself.
She believes the GPs should be sending reminders to people just so it doesn't "slip through".
She also said new parents need to be more informed on why their kids need vaccines so they don't fall trap to anti-vaxxing scare campaigns.
"If people don't know what vaccines are given in children they might be nervous to do it," she said.
Another mum told ITV News: "You could have a bit more support for why they have it, I think you're just told that they should have it, not for the reasons why.
"But I think there is [enough information], but on my part, I could have researched it more, instead of just being told they should have it.