Mr Johnson's wife had pleaded for his release on Arabic TV
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A man's head discovered during a police raid in Riyadh earlier this week is that of American hostage Paul Johnson, the US embassy in Saudi Arabia says.
"We did see the head... and have confirmed that it is the head of Paul Johnson, unfortunately," spokeswoman Carol Kalin told the AP news agency.
Paul Johnson was abducted by militants linked to al-Qaeda on 12 June.
Photographs of his beheading were published on an Islamist website six days later.
Militants arrested
Johnson, 49, was from New Jersey and had been working as a helicopter engineer in Saudi Arabia for US defence contractor Lockheed Martin.
His head was discovered in a refrigerator after Saudi police stormed an apartment in Riyadh, killing two suspected militants.
Security forces also found a surface-to-air missile, rocket-propelled grenades, automatic rifles, pistols, hand grenades, ammunition, computers, cash and nitrates and aluminium powder.
A video apparently showing Johnson blindfolded appeared on an Islamist website.
His kidnappers, a group calling itself the "al-Qaeda Organisation in the Arabian Peninsula", had demanded the release of prisoners arrested in Saudi Arabia for links to radical Muslim groups.
After the deadline for their demands passed, graphic images of Johnson's beheading appeared on a website linked to Islamist militants.
Johnson was the second US civilian to have been beheaded by his abductors in the region this year.
Businessman Nick Berg was killed by militants in Iraq in May.