Wales were awful in defeat to Argentina last weekend, and there was no improvement in a demoralising 26-19 loss at the Millennium Stadium from the Six Nations champions, who now face the ominous task of meeting world champions New Zealand in eight days' time.
Leigh Halfpenny kicked four penalties and converted Ashley Beck's first-half interception score, but it was not enough as Samoa gained revenge for their World Cup reverse of 13 months' ago.
The writing had been on the wall when Fa'atoina Autagavaia crossed for the visitors after just 64 seconds, with second-half tries from George Pisi and Johnny Leota sealing the win and Tusi Pisi kicking 11 points.
Wales could hardly claim to have been caught unawares by Samoa; the previous two meetings between the sides had seen them scrape home by 17-10 and 17-13 verdicts.
The result leaves Wales in real danger of slipping out of the top-eight in the IRB world rankings, which could leave them facing a nightmare draw for the 2015 World Cup. A win for Scotland over South Africa on Saturday will drop Wales to ninth.
Howley said: "I have spoken to the players and we are obviously disappointed as a coaching team and group of players.
"International rugby is about discipline and when we created opportunities in the game, although we did not have many, we were disappointed in terms of our top-three inches at times.
"We were outperformed by a Samoa side whose ability to keep the ball better than us was the most disappointing aspect of the performance.
"We did not have control of possession or in terms of the contact area and that (performance) is obviously not international standard."
British & Irish Lions head coach Warren Gatland will return to take the reins next week, but the Kiwi faces a huge task to turn around Wales' alarming demise before the All Blacks arrive in town.
On this evidence it is difficult to see Wales having any hope of living with Richie McCaw, Dan Carter and company.
But Howley believes the challenge ahead represents an ideal opportunity for Wales to get back on track.
He said: "Over the last 12 months we have been to the World Cup semi-finals and won a Grand Slam. We have had the highs and now we are going through a low.
"We have to bounce back and rugby gives you an opportunity.
"This group of players have been outstanding in training, but when we cross that white line our skills are not up to scratch of international rugby at this moment in time, but we will keep working hard and keep working smart and we will stick together.
"We have two good games against New Zealand and Australia to come and it is something to look forward to."
Wales may also be counting the cost of further injuries after hooker Richard Hibbard, fly-half Dan Biggar (both shoulder) and lock Ian Evans (knee).
The manner of the injuries suffered by Hibbard and Biggar may yet occupy the attention of citing commissioner Paul Minto.
Hibbard was felled by a crunching tackle from the outstanding Taiasina Tu'ifua, in which the Newcastle number eight did not appear to use his arms, and eventually forced off to have his arm put in a sling.
Biggar, meanwhile, was on the end of a reckless challenge from Teofilo Paulo, in which the lock led with his head.
Hibbard's replacement Ken Owens was also dragged to ground by the neck by Maurie Fa'asavalu.
With Adam Jones, Dan Lydiate, Alun Wyn Jones, Matthew Rees and Jonathan Davies all injury absentees, Wales cannot afford to lose
Howley said: "Dan and Richard have taken blows to their shoulders.
"It is not the time to discuss anything, but I don't think they were legal tackles as far as we are concerned having looked at the footage.
"It is disappointing to lose players. Dan and Richard had been given an opportunity and Ian Evans has hurt his knee. But it might give someone an opportunity next week."
Samoa captain David Lemi hailed his side's win, but also accused Wales of being predictable in attack.
The Worcester wing said: "This was a big opportunity for us to have a good ranking before the World Cup draw and credit to the boys today, we came out on top.
"We have been watching Wales since the World Cup. They did the same thing they used in the Six Nations and against Argentina. We knew if you stop their go-forward men, you stop their game.
"If you dominate the scrum and line-out the other side cannot play rugby."
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