Almost a quarter of teachers from across more than 2,200 mainstream primary and secondary schools also believed boys had fallen further behind than girls.
The National Foundation for Educational Research’s (NFER) survey comes as many students return to classrooms this week for the first time since lockdown.
Its study found that as of July, teachers had on average covered 66% of the curriculum during the 2019/20 academic year.
Teachers estimated on average that their pupils were three months behind in their studies, the survey said.
However, more than half (53%) of those teaching in the poorest schools in England reported their students were “four months or more” behind in their learning, compared to 15% of teachers in wealthier settings.
The survey also found that the learning gap between disadvantaged pupils and their better-off peers had increased by 46%, adding that the figure was likely to be an "under-estimate".
Dr Angela Donkin, chief social scientist at NFER, said: "Whilst it is crucial that children catch-up, we should not assume that teachers will immediately be able to deliver the same quality of teaching, at the same speed, as before the pandemic.
"There remains a range of barriers for teachers and schools, which means catch-up should be seen as part of the ongoing process of learning recovery, for most pupils, rather than as a quick-turnaround solution."
She said it was "clear" that additional support needed to be targeted at disadvantaged pupils and schools in the poorest areas.
The majority of pupils had been expected to learn at home throughout the 2019/20 summer term, but teachers reported that only 38% returned their last piece of set work in July, compared to 42% in May.
School leaders said that just over half of students who were eligible to return did so, with those from black, Asian and minority ethnic (BAME) backgrounds having lower attendance at 49%.
Almost a third of school leaders said safety concerns from parents were a common reason for their children not attending.
Almost three quarters of teachers did not feel able to teach to their usual standard while the coronavirus regulations were in force, the survey found.
In an open response question, 49% of 1,034 teachers whose teaching was affected said distancing requirements had a negative impact on areas such as group work and their ability to interact with pupils properly.
More than half of school leaders also reported that they were using teaching assistants to lead classes.
Teachers estimated that 44% of their pupils will need "intensive catch-up support", the survey said, with the percentage increasing to 57% in the most deprived schools.
NFER’s list of recommendations included the need for schools to receive further support to manage pupil non-attendance and more money to help with managing coronavirus safety measures.
By Luke Powell, PA