Justin Laurens Stein, 31, was on Thursday charged with two counts of possessing an unregistered firearm, two counts of possessing an unauthorised firearm, possessing ammunition without licence or permit and aggravated break and enter in company.
He was also charged with two counts of possessing child abuse material for unrelated matters.
Stein, who is in custody, is due to appear before Penrith Local Court on Friday.
The girl was reported missing on January 14, while holidaying at Wildenstein Private Gardens at Mount Wilson.
A five-day search of bushland ended with her body being found in a barrel dumped near the Colo River northwest of Sydney.
NSW Police later said an autopsy found she had died of a gunshot wound.
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