In addition to his trip to South Africa, Prince Charles traveled to India and Sri Lanka for the Commonwealth Heads of Government meeting with his wife, Camilla, the Duchess of Cornwall, at a cost of £434,000.
Read MoreTime for lodgers, Your Majesty? Royal budget woes
On top of the high travel expenses was a 45 percent rise in property maintenance carried out by the royal estate. This included a £3.4 million refurbishment job to the official residence of Charles and Camilla, which the report said was "uninhabitable" previously.
The monarchy cost each Briton 56 pence in the past financial year which Buckingham Palace insists represents "value for money."
But some opponents of the royal family have accused them of "spin" over their financial record.
"The job of reporting royal finances needs to be taken out of the hands of the palace and given to some honest brokers," Graham Smith, CEO of the antimonarchist group Republic said in a statement.
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"The spin has to stop, the excuses have to stop, the royals need to be held to account for their profligacy."
Earlier this year, British lawmakers slammed Queen Elizabeth for overspending her budget and urged her to rein in spending.
Royal property booming
Meanwhile, the queen's property portfolio has posted record profits of £267.1 million in the latest financial year, up 5.7 percent from the year before, thanks to a boost given by soaring London real estate prices.
The Crown Estate is a commercial business run by an independent board. All the profits are paid to the U.K. Treasury, which uses this money to determine how much to grant the royal family each year.
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The estate saw the total value of its assets rise 14.6 percent in the 12 months to March 31, hitting £9.9 billion. At the same time, the company has been slimming down with disposals totaling nearly half a billion pounds.
The surge in value was driven by the high demand for office space in London's West End, where much of the portfolio is concentrated and rents are very high.
Properties in its portfolio include offices in prime locations such as London's Regent Street, as well as shopping developments across the country. The Crown Estate signed a new partnership with Oxford Properties, a major Canadian real estate investor, to carry out a £320 million refurbishment of the St. James Market development.
The business has also been investing in offshore wind farms which helped generate over £15 million of revenue, up 46 percent from the £10.6 million the year before.
Correction: The version corrected the amount in the headline to $433,000 for the Mandela funeral trip.
—By CNBC's Arjun Kharpal