National Security Council spokesman Michael Anton also said that with Pakistan the "business as usual as it has been up to now is over."
"The important takeaway for the Pakistani government last night is that, you know, they should understand that they're on notice from this president, from this administration," Anton was quoted as saying by Politico.
"The US has been really patient with Pakistan for a really long time. We haven't been getting a good deal from them," he added.
The official said that the onus for improving the relationship is now on Pakistan.
Anton said the president had benefited from an outsider's perspective on the US-Pakistan relationship, eschewing the conventional wisdom that "however much the Pakistanis double- deal you and lie to you and don't cooperate, you have no choice but to just keep the status quo."
"How do we get the Pakistan to behave better? The answer is we have leverage points over Pakistan that the strategy contemplates we will use. Ultimately whether they behave better or not is completely up to them," Anton said.
"If so, that's a choice that they will make and then we will make choices based on their choice," Anton said.
Observing that the US gives the Pakistani government substantial security aid, Anton said, and in return receive, at best, "indifference to border crossing and terrorist safe havens and sanctuaries" in Pakistan's tribal regions along the Afghan border.
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