Companies House collected £82.3 million in the 2012/2013 financial year, up from £53m in 2007/08.
In the first three months of the current financial year, however, fine collection has eased from £20.6m to £20.1m compared with the same period last year.
Corporate law experts at Pinsent Masons say a more stringent penalty regime is responsible for the sharp increase, with SMEs suffering the most as they grapple with increasingly complex accounting requirements.
In 2009 Companies House revised its penalty regime for late filing, at the same time as public and private companies felt the impact of a reduced time frame in which documents must be submitted to the registrar.
Companies House can now multiply any outstanding penalties issued to companies that consistently file annual accounts after the deadline, effectively aggregating fines.
Pinsents said the issue seems to be particularly acute in Scotland, where the value of penalties collected increased by 75% since 2007/08, compared with 54% in England and Wales.
Business Secretary Vince Cable has launched a consultation on further measures to improve transparency in business, imposing tougher rules on public and private companies in the UK.
Pinsents said the new rules are hitting SMEs the hardest as they struggle to cut through red tape and an onslaught of new regulation. New rules on directors' reports and board remuneration arrive in October.
Martin Webster, partner at the firm, said: "Unlike large scale companies, capacity is an issue and it's unsurprising that smaller companies fail to hit Companies House deadlines and then suffer the consequences.
"High standard of transparency are one of the defining characteristics of UK Plc. The question now must be whether a more appropriate balance can be struck between corporate bureaucracy and targeting those who disregard the rules."