The Olympic gold medallist leaped 8.51m at a meet in California last week but amid the celebrations his feat was questioned by rival Chris Tomlinson.
Tomlinson, who previously shared the record with Rutherford, said pictures showed the jump was "not legitimate" and he reckoned Rutherford had overstepped at take-off by some distance.
Tomlinson had also suggested that the competition in San Diego had become a laughing stock after the jump was allowed to stand.
"Lots of people have been sending me pictures of Greg's jump and what they show is that Greg's foot is not marginally over the plasticine but significantly over," said Tomlinson.
"It's left me in a slightly awkward situation because it's a jump that's clearly a large foul in a competition that isn't a world championships, isn't an Olympics or a grand prix. It's a very small competition and where do we draw the line in the sand?
"The long jump world are up in arms about this, texting and tweeting me and saying: 'How is this allowed? This is wrong.' Down at the local track the officials would be far more suited to a professional environment than what that particular competition was."
However, USA Track and Field, which officiated the event, said: "The meet was USATF sanctioned, through our USATF Southern California Association, and used USATF officials. Thus all marks are verified and legal."
And Rutherford was adamant his record should stand, saying: "All the right i's were dotted and t's crossed. Ultimately, I wouldn't do it if it was not an official competition because the risk of jumping well and it not being official would absolutely gut me."
Despite the accusations, Tomlinson, who had initially congratulated Rutherford on Twitter when the jump was made, stressed that he has the utmost respect for his rival and regarded him "as a friend".
Rutherford will have a chance to put the controversy to bed when he competes in Manchester on May 17 as part of his Commonwealth Games build-up.
- Sports & Recreation
- Chris Tomlinson