As far as i remember Voldemort didn't know Dumbledore was in the ministry when he arrived.
He saw Harry wide open after he had just tried the cruciatus curse on Bellatrix.
I'm sure when he appears Bellatrix tries to warn Voldemort but he doesn't listen.

'Master, you should know -'
'Be quiet Bella,' said Voldemort dangerously. 'I shall deal with you in a moment. Do you think I have entered the Ministry of Magic to hear your snivelling apologies?'
'But master - he is here- he is below-'
Voldemort paid no attention.
'I have nothing more to say to you, Potter,' he said quietly. 'You have irked me too often, for too long. AVADA KEDAVRA!'

Harry had not even opened his mouth to resist; his mind was blank, his wand pointing uselessly at the floor.
But the headless golden statue of the wizard in the fountain had sprung alive, leaping from its plinth to land with a crash on the floor between Harry and Voldemort.
The spell merely glanced off the chest as the statue flung out it's arms to protect Harry.

'What -?' cried Voldemort, staring around. And then he breathed, 'Dumbledore!'

Voldemort had no idea that Dumbledore was there.