The June Purchasing Managers Index rose a little but remained in the negative range at 48.6.
Figures below 50 indicate a contraction.
Markit said Britain's PMI hit a 10-month high in March and a three-year low in May at 45.9.
For the second quarter of the year, the PMI averaged 48.2, the weakest quarterly average since the second quarter of 2009.
"Manufacturing is seeing lots of volatility at the moment, due to factors such as the jubilee holidays, making it very difficult to see what the underlying trend is," Markit economist Ron Dobson said in a statement. His "jubilee" reference was to the queen's Diamond Jubilee observation.
"However, there is no denying that the second quarter as a whole is looking weaker than the first quarter," he said.
In June, the production index rose for the sixth month out of the past seven, "but only following a solid contracting during May," the report said.
New orders in June remained in contraction for the third consecutive month.
"The manufacturing sector is playing catch-up after the dramatic falls in activity reflected in last month's PMI," said David Noble, chief executive officer of the Chartered Institute of Purchasing & Supply.