Only 76% of Luton primary school pupils are attending good or outstanding schools, according to the Ofsted annual report 2013/2014, released last week.
It also revealed that 83% of secondary school pupils are attending good or outstanding schools.
The report said that inspectors had found that in the East of England, primary schools were getting better but improvements in secondary schools had stalled.
A spokesperson for Luton Borough council said: “We are delighted to see Luton recognised as having the second highest proportion of good and outstanding secondary schools in the East of England and that progress in mathematics in these schools places Luton in the top 25% nationally.
“Luton was the only authority in the East of England that exceeded the national level for the proportion of children entitled to free school meals attaining at least five GCSEs at grades A*-C including English and mathematics.
“In the primary sector the proportion of good and outstanding schools has risen by 6% over the last year and this places Luton 5th out of the 11 Eastern Region Authorities.
“Attainment and progress at Key Stage 2 in primary schools although improving remains below the national average and this remains a priority for the council.
“The KS2 performance data for Luton schools is inaccurate as it fails to take account of the results of one large primary school.
“The results for this school were released after the data base for this report had been closed. When the data base is revised Luton’s KS 2 results will increase in reading and mathematics.”