The £300m development was targeted a day after an approved security firm started guarding the area.
A digger was destroyed in the attack.
Milne Management security, which won the contract, is approved by the Security Industry Authority. It had previously reported Gard, a rival firm, to the police over an alleged approach to provide services.
Gard, which has denied any involvement in the attack, was banned from bidding for the new contract by Glasgow City Council because it is not a member of the SIA’s approved contractor scheme.
Gard already protects the National Indoor Arena and National Velodrome in the city, contracts won before the rules changed. However, they are expected to conclude next year.
The news follows the story in The Herald last week that revealed Strathclyde Police has written to Scotland’s largest health board warning it against going ahead with a £2m taxi contract to a firm previously linked to organised crime.
Kenny MacAskill, the Justice Secretary, is keen to prevent any organised criminals muscling in on public contracts.
To become an approved contractor, firms must now meet a list of strict criteria, including that those who run companies are “fit and proper”.
Last year, Glasgow City Council launched a crackdown on firms with gangland links from cashing in on the Games and the rules are expected to be made even tighter.
At least one petrol bomb was thrown at machinery on the site of the village in Dalmarnock on September 7, the day Milne Management security staff began its contract.
The following night, the digger was wrecked on the land, which will be home to 8000 athletes in 2014.
A spokesman for Strathclyde Police said: “We received a report of a wilful fireraising of plant equipment. Inquiries are continuing. No one has been arrested at this time.”
A city council spokesman said: “The National Indoor Arena and National Velodrome security contract was awarded before the introduction of the requirement that 2014 security companies should be SIA approved contractors. We have since introduced a new process which makes it far less likely that firms who are not run by the appropriate type of people would be able to get work.”
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