Pakistan's allegations come months after both Canada and the United States separately accused Indian agents of being linked to assassination attempts on their soil.
The tit-for-tat strikes are the highest-profile cross-border intrusions in recent years, raising alarms for the rest of the Middle East.
"Pakistan is a major non-NATO ally of the United States. That will remain the case, but we would urge restraint in this case," a State Department spokesman said.
The series of attacks threaten to escalate tensions between the countries and escalate tensions in South Asia.
Iran said on Tuesday it had targeted Israel-linked militant bases inside Pakistan.
The foreign ministry said Iran's strike on targets in Pakistani terrritory was an unprovoked and blatant breach of Pakistan's sovereignty and was "unacceptable."
Iran's Revolutionary Guard attacked targets in Pakistan just one day after shelling Iraq and Syria with missiles.
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