The Ryedale side lost 28-13 at relegation rivals Morpeth, a result which moved the home side out of the bottom three.
Morpeth are now one point above the danger line with a game in hand, leaving Malton with five games to salvage their season.
The visitors had led 13-10 in the early stages of the second half, but Morpeth responded by taking the game out of Malton’s reach.
James Bulmer kicked Malton into a 3-0 lead, but the home side got a converted try midway through the first half thanks to a pick and drive.
A Bulmer penalty kick rebounded off a post but he was successful with another kick before Morpeth made it 10-6 at the break with a penalty.
Malton took the lead five minutes into the second period when Jamie Rounthwaite won clean ball from a lineout and fed prop Ed Gwilliam, who burst through before handing on to flanker Ali Coe to crash over.
Bulmer converted, but the advantage was short-lived as Malt were penalised for an offside and the scores levelled.
A Morpeth winger then burst through two weak tackles to touch down in the corner and a penalty gave Morpeth a healthy cushion.
Deep into added time, a series of drives near the Malton line produced the final score of the game for the home side.
Pocklington battled gamely but lost 43-20 a home to to North One East champions-elect Cleckheaton.
Cleckheaton opened the scoring with an early penalty which home full-back Jack Fletcher equalised in the ninth minute.
The visitors scored two converted tries to lead 17-3 at the break.
Pock wing Charlie Allen dived under the posts and Fletcher goaled, while a Fletcher penalty made it 17-13.
The visitors then bagged two converted tries in three minutes and they added two more late scores.
Winger Billy Hardy plunged over for Pock and Fletcher converted.
Selby moved back up to fourth in Yorkshire One with a heart-stopping 39-31 victory at home to Pontefract.
Josh Cruise missed a kickable penalty after one minute and Pontefract took the lead four minutes later through centre Chris Sant.
Selby hit the front after nine minutes with a magnificent run by number eight Martin Protheroe, beating five defenders before touching down near the posts to give Cruise an easy conversion.
Another Cruise penalty miss after 20 minutes was followed by an excellent break from the fly-half, who scored a try and kicked the goal.
An awful long throw by Selby at a lineout gifted Pontefract possession and centre Glenn Boyd went over for a try which he converted. Pontefract’s Matt Williams was yellow carded for a high tackle on 29 minutes and Cruise kicked the penalty.
Selby then scored the try of the match when a superb passage of play resulted in flanker Jacob Robinson going over near the posts. Cruise converted for a 24-12 lead.
Flanker Joe Perkins scored for Pontefract on the stroke of half-time and Boyd converted, but Selby crossed first in the second period through winger Kevin Lamb.
Ponte replied with fly-half Craig Fawcett going over after 51 minutes, with Boyd converting.
With Selby’s lead down to three points, another superb 58th-minute try from Protheroe, which Cruise converted, gave them breathing space.
On 73 minutes, a smart Josh Cruise drop goal increased the lead and Pontefract could only add a 78th minute try by Fawcett.
York topped pool two in the Intermediate Cup with a 34-7 victory at Consett.