The Environment Contract was designed to make government policy more open, but hackers left some embarrassing editing throughout the site and a swastika was reportedly added to one page.
Environment Secretary David Miliband admitted that there were risks to the process before it started.
"This is new territory for the government, and it involves a fair bit of trust," he said on his official blog.
"As anticipated, we have had some problems with accidental or malicious editing or removal of material. We may have to adjust our approach."
The website was eventually taken down after 170 people made 'additions'.
The wiki was edited to include advice for citizens to "pay a higher proportion of their income to the government, and see little tangible improvement in their standard of living".
The tools needed to bring about this change were listed as "spade, organic yoghurt stirrer, old washing up liquid bottle, sticky-back plastic".
Following the attacks Miliband acknowledged that the "extreme openness" of the wiki had already lead to some practical jokes and the swastika.
"Strange how some people get their kicks. But the experiment will continue," he insisted.
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