On-loan Doncaster midfielder Dave Syers scored twice as Scunthorpe began life after Brian Laws with a morale-boosting victory, while the hosts were booed off at full-time by a crowd of almost 15,000 at Fratton Park.
Whittingham, summoned to crisis talks by the board after last weekend's 4-0 thrashing at AFC Wimbledon, said: "I understand the fans booing, they are frustrated and I am frustrated.
"But we are 16 games into a season with a team that has been completely rebuilt with 16 new players.
"We told people all along it is going to take time and it will. I do not think the effort is missing; it is just not coming together.
"Going forward we looked good but defensively we were not so good. We don't defend our goal well enough and the organisation is not good enough.
"I thought we played well on the ball and created opportunities. It is the other end we have got to get it right."
Scunthorpe, who sacked Laws after the midweek 2-1 FA Cup defeat by Grimsby, spurned several good chances before Tom Craddock headed Portsmouth into a 36th-minute lead.
The home side's first meaningful attacking move ended with Craddock claiming his first goal for the club from a Ricky Holmes cross.
Pompey's lead lasted only four minutes, Syers equalising at the far post after Andy Dawson's corner found its way through the six-yard box.
Deon Burton was the culprit as Scunthorpe bungled more chances before Syers grabbed their winner after home goalkeeper Trevor Carson had spilt Sam Winnall's left-foot shot into his path.
Portsmouth twice hit the Scunthorpe woodwork but Carson twice made fine saves to deny the visitors, for whom Winnall struck the outside of the post.