Krishna statement comes after his junior Shashi Tharoor had publicly questioned the new visa rules.
Krishna said there could be different perceptions but there is also a method and procedure to "sort out" those issues.
When asked if Tharoor and the Ministry were on the same page, Krishna said, "The broad policy parameters are dictated, decided by the Minister in-charge of External Affairs of this country and everyone will have to fall on the same page."
About repeated controversies over Tharoor tweeting, Krishna said, "I would request you to not generalise issues. There could be different perceptions.
Replying to a question if as the boss of the Ministry, he was happy with the outcome of the meeting with Tharoor, Krishna said, "Oh yes. As the boss of the Ministry, as head of External Affairs Ministry, I am completely at peace with myself and the Ministry. Everything is alright."