The information obtained through a freedom of information request made by business law firm, DWF, also found 60% of inspections in this period resulted in a charge to the business.
Under the Health and Safety (Fees) Regulations 2012, which came into effect in October 2012, those who are found not to be compliant with health and safety laws are liable to recovery of HSE's related costs, including inspection, investigation and taking enforcement action.
The total figure is around £100,000 higher than the first invoice run in October and November 2012, and included more than 1,800 invoices - nearly 500 more than those issued during the first period.
There was a significant increase in FFI time recorded against manufacturing businesses, which accounted for 43% of the total, followed by the construction sector, which received nearly 30% of the total number of invoices.
Despite the waste management sector being high on the HSE priority list, given the sector's high fatality rate, only 63 invoices were issued against businesses in the water and waste management sector, which could demonstrate either a high level of compliance in the sector or a low inspection rate.
Steffan Groch, head of regulatory at DWF, said: "The number of invoices is increasing at an alarming rate and it is now more likely than ever before that business owners will receive an HSE inspection that results in an invoice for the HSE's time.
"There is still a worry though that queries are not being dealt with independently. The HSE handles its invoices directly, which some might say is like parking wardens dealing with queries on the tickets they have issued."
Groch added: "We encourage the HSE to review its appeal process to ensure they are dealt with in a fair and transparent manner."
