Microsoft Corp. says 5 percent of Windows computers scanned with its new free malware cleanup tool were infected, the company says.

Microsoft’s free Safety Scanner, which relaunched May 12, was downloaded 420,000 times the first week of its release and cleaned malware from 20,000 Windows PCs, a 4.8 percent infection rate, according to Microsoft’s Malware Protection Center.

The average infected PC had 3.5 threats removed. Seven of the top ten malware infections were Java exploits, MMPC reported in a blog post.

Microsoft says two holes in Java account for 85 percent of all Java attacks in the second half of 2010, when Java exploits exploded from 1 million in the first six months to 13 million in the second half of the year.

Both vulnerabilities in Java have since been fixed. But they were still number one and number six in the Safety Scanner top 10 infections, says Microsoft.

The free safety scanner expires after 10 days and must be redownloaded with updates, not exactly the most efficient of systems, but free is free.

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Tags: 1 in 20 Windows PCs infected with malware, Internet, Java exploits, Microsoft Safety Scanner, Security