"The United States is determined to hold to account anyone who commits crimes against Iraqi people," Mr Biden added.
"While we fully respect the independence and the integrity of the US judicial system, we were disappointed with the judge's decision to dismiss the indictment, which was based on the way some evidence had been acquired."
Iraq maintains the Blackwater guards fired without provocation. Blackwater said the firing followed an ambush on one of its convoys.
The US rejected attempts for a trial in Iraq but charges in the US were thrown out when a judge ruled in December that the guards' constitutional rights had been violated and that the justice department had mishandled evidence.
The ruling provoked anger in Iraq and this month the Iraqi government began collecting signatures for a class action lawsuit on behalf of people killed or wounded in incidents involving Blackwater.
Iraq said it would seek compensation for a number of such cases and would continue to "act forcefully and decisively to prosecute".
The 2007 incident caused widespread public anger against foreign security companies operating in Iraq and their activities have been severely curbed since then.
Mr Biden's comments came as he tried to defuse a political crisis over the banning of more than 500 candidates in the March election, many on suspicion of loyalty to Saddam Hussein's dissolved Baath Party.
Many Sunnis are outraged, saying their community is being marginalised, but many Shias are adamant Baathists cannot be rehabilitated.
Mr Biden met PM Nouri Maliki and President Jalal Talabani among others.
Mr Maliki, a Shia, has generally backed the disqualifications but Mr Talabani, a Kurd, has questioned the legality of the commission which issued the disqualifications, referring it to the supreme court for a ruling.
Mr Biden said he was confident there would be a solution.
The BBC's Jim Muir in Baghdad says both the US and UN are increasingly worried that the March elections could become discredited.
He says the Americans will be eager for the elections to foster national reconciliation so the withdrawal of troops can be achieved against a stable background.
Although violence has lessened in Iraq over the past two years, security remains fragile.
Both Iraq and its Western backers see the March election as a crucial test of whether peace can be made sustainable.
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