The hearing started just after 10:00 in Pretoria but commission chair Judge Willie Seriti agreed to a two-week adjournment so that documents could be declassified.
"There is a question of the classification of documents, you will know there are considerable difficulties which are attached to the production of documents [which are classified] which are appropriate for the commission," said Michael Kuper, SC, lawyer for the defence department.
The commission will look into allegations of fraud, corruption, impropriety or irregularity in the 1999 deal.
Jacob Zuma, whose financial advisor Schabir Shaik was convicted of corruption over his part in the arms deal, announced the investigation in 2011.
The controversial Strategic Defense Procurement Package was supposed to modernise South Africa's defences through the purchase of fighter jets, submarines, corvettes, helicopters and tanks, and involved companies from Germany, Italy, Sweden, Britain, France and South Africa.
The United Kingdom's Serious Fraud Office suspects that bribes of over R1 billion were paid to facilitate deals to buy Hawk trainer aircraft and Saab Gripen fighter jets.
The inquiry was adjourned to August 19 and the public hearings, which were supposed to start in March, are set to run until January 2014.
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