It depends whether it is the beginning or end of the conversation.
"I'm sorry to have disturbed you "is fine at the end of the conversation. If you have disturbed someone while they are working to ask them a question, for example, you could end the conversation in this way.
If it is the beginning of the conversation, you could approach your colleague, for example, with the words 'I'm sorry to disturb you, but...'
Your second suggestion doesn't work, I'm afraid.
Alternatively, you could say 'I'm sorry for disturbing you'. The beauty of this phrase it that it works for both the beginning and end of the conversation.
I hope that helps.