The employee, who wished to remain anonymous, was working at Swan Mill's Swanley warehouse when he was crushed against a pallet of paper goods by a reversing forklift truck.
The accident, which happened in October 2011, resulted in the member of staff suffering three fractures in his right ankle and two fractures in his left leg. He returned to work on 9 January this year.
Swan Mill Paper Company was fined £5,000 and ordered to pay £3,069 in costs at Sevenoaks Magistrates Court on 7 May, after admitting a breach of workplace regulations.
HSE Inspector Guy Widdowson said the incident had been entirely preventable.
"Swan Mill Paper Company failed to make sure that there was a safe vehicle and pedestrian system of work in place within their warehouse," he added.
"Such a measure would have prevented vehicles being able to access areas where workers on foot were moving around. Such a system was entirely possible without any detriment to the work being done."
Widdowson said that the risk of a collision between a moving forklift and a warehouse operative while both were working in the same location was significant and as such "should have been obvious to the company".
A statment issued by Swan Mill said: "On 12 October 2011 a Swan Mill Paper Company employee was injured in an incident at our site. The welfare of our staff is of the utmost importance and we deeply regret this incident.
"We are a family-run firm and we take the safety of all of our 231 employees very seriously. This is the first time such an incident has occurred on our site. Our employee has returned to work with our full support. He continues to recover from his injuries and we are doing all we can to support and assist him.
"The health and safety procedures that applied on the day of the incident have been in place for many years and there had been an estimated 26 million truck movements without incident prior to his unfortunate accident occurring.
"We took immediate remedial action at the site and have cooperated fully with the HSE. One of our first steps was to make a proactive recommendation to the HSE about additional safeguards. These were accepted in full by the HSE.
"As today’s ruling makes clear, we have not contested the charge. Welfare and safety of our staff is paramount and we now have even more robust health and safety procedures in place."