It emerged on Sunday that the 54-year-old former striker was in discussions with the club he briefly represented as a player over a role working alongside his former Wimbledon manager.
But the 54-year-old last month joined the coaching staff at Millwall, and he told Sky Sports News: "After meeting with Mike Ashley and Joe Kinnear, I made the hard decision that it is not the right time for me to take up this role.
"It was an honour to be asked to work at a fantastic club and I have the utmost respect for the Newcastle United and its fans.
"I am currently enjoying a role helping out at Millwall, but would like to thank Mike Ashley and Joe Kinnear for the opportunity."
It had been suggested that Harford would concentrate on the domestic market, helping Kinnear to identify potential targets from the lower leagues and monitoring those players sent out on loan by manager Alan Pardew.
However, news of the talks sparked further claims that Pardew was being undermined amid accusations that owner Mike Ashley was installing a shadow management team above him.
The manager and his players are currently in Portugal, where they are continuing their preparations for the new season following a 3-1 friendly defeat by Rio Ave on Saturday evening.
Kinnear, who was put in charge of all football-related matters when he was controversially appointed to his new post by Ashley, is currently attempting to implement the transfer plan put in place after discussions with Pardew and chief scout Graham Carr, although the Magpies remain the only Premier League club yet to sign a senior player this summer.
But that could change in the near future with the club understood to have formalised their interest in Lyon's France international striker Bafetimibi Gomis, while Aston Villa's Darren Bent remains firmly in their sights despite reported interest from Fulham.