Cipriani has been left out of the 36-man squad that will begin preparations for the autumn internationals at a training camp in Portugal next week despite excelling for Gloucester so far this season.
The 30-year-old was named Gallagher Premiership player of the month for October and is the incumbent fly-half after starting England’s most recent Test against South Africa in June.
Jones has watched him four times this season, however, and rates him beneath Owen Farrell and George Ford in the position’s hierarchy.
“It’s tough on Danny,” said Jones, who has previously stated that Cipriani’s conviction for common assault and resisting arrest in August has not impacted selection.
“I rang him on the phone. Whenever you tell a player they’re not in the rest of the conversation is a bit of a blur.
“Have you ever had a girl tell you that she doesn’t love you? You don’t remember the rest of the conversation.
“It’s like that with a player – when you tell them they’re not in, they say ‘yes, yes’, but they don’t hear anything.
“There are areas he needs to work on and I’ve made those very explicit to him. He understands that and needs to keep working on them.
“It comes down to a judgment. People think he played well; well maybe I don’t think he plays that well.
“That’s a judgement and at the moment my judgment is the most important judgment.”
Another player missing from the 36 who will travel to Portugal for next week’s pre-series training camp is Joe Marler, although his absence is self-enforced.
Marler has retired from international rugby in order to spend more time with his family, adding that he has struggled to deal with the anxiety caused by being away from home.
With Mako Vunipola missing the autumn due to a calf injury a void has been created at loosehead prop that will be filled by rookies Alec Hepburn and Ben Moon, so Jones would welcome a change of heart from Marler.
“Joe has made his decision, to me, in a very logical and coherent way. Good luck to him,” Jones said.
“But I’ve told him the door is always open. If he changes his mind – and people do – the door’s still open.”
For the first time in Jones’s reign, Dylan Hartley must share the leadership duties after being named co-captain alongside Owen Farrell.
Since the 2015 World Cup Hartley has been England’s automatic pick in the role when available, but now Farrell has been promoted after deputising during the summer tour to South Africa.
“It’s the best situation for us and we’ll use it in November. If it’s right going forward we’ll take it right through to the World Cup,” Jones said.
An additional first since England 2015 is the return of Ben Morgan, who is called up to fill the gap at No 8 left by injury and suspension that has accounted for Billy Vunipola, Nathan Hughes and Sam Simmonds.
England squad – Forwards (20): T Curry (Sale), C Ewels (Bath), J George (Saracens), D Hartley (Northampton, co-capt), A Hepburn (Exeter), T Hill (Worcester), M Itoje (Saracens), G Kruis (Saracens), C Lawes (Northampton), Z Mercer (Bath), B Moon (Exeter), B Morgan (Gloucester), M Rhodes (Saracens), N Schonert (Worcester), B Shields (Wasps), K Sinckler (Harlequins), E Stooke (Bath), S Underhill (Bath), H Williams (Exeter), M Wilson (Newcastle).
Backs (16): C Ashton (Sale), M Brown (Harlequins), D Care (Harlequins), J Cokanasiga (Bath), E Daly (Wasps), N Earle (Harlequins), O Farrell (Saracens co-capt), G Ford (Leicester), A Lozowski (Saracens), J May (Leicester), J Nowell (Exeter), H Slade (Exeter), B Te’o (Worcester), M Tuilagi (Leicester), R Wigglesworth (Saracens), B Youngs (Leicester).