MY CX9 2009 Is getting some vibrations on 6th gear, while shifting from 5 to 6 and 6 to 5. it happens on low acceleration positions. if i give full acceleration the gear moves smoothly.

i Had tried in Manual mode by shifting upwards and there is no vibrations.

That means the vibration is only in Auto mode.
The axle is fine, boots and joints are fine, tyres are balanced, Gear oil and engine oil is new.
What could be the reason

 

How many miles? Are you original owner?

 

I am the second owner
The car is now on 156000 km
The vibration is noticeable on slow gear shifting. if i accelerate the gear is shifting smoothly
There is no vibrations on Manual mode if i shift the gears up.
The transmission fuel and engine oil is changed recently

 

If it was mine, I would check the fluid level and check the condition of the oil. Then I would drop the pan, fluid/filter change and see if that changes anything. Not much else you can do short of a tranny overhaul. Good luck finding a shop you can trust with that.