DP World, of the United Arab Emirates, said on Thursday night it would go ahead with a $6.85 billion deal to acquire the port operations worldwide of P&O but would make arrangements for the US ports involved while it discussed security concerns.
A political uproar ensued over the deal, which the White House approved without congressional oversight.
The company said in a statement: "In practice, this will mean that DP World will not exercise control over, or otherwise influence, the management of P&O's US operations pending the outcome of these further discussions."
The issue blew up in Washington over the past week with many senior figures in Bush's Republican party, as well as Democrats, vowing to stop the deal because it could threaten US security. They said they should have been informed about it in advance.
Tough on security
Bush insisted the deal was safe and that the company's home base, the UAE, was a close ally in his "war on terror".
But other Republicans feared it would undermine the party's image as tough on security before this year's congressional election.
A US politician opposed to the takeover said: "We're still going to have to get an analysis of the firm itself to make sure that it has no al-Qaida connections and that no one in the government with al-Qaida connections would have any influence over the firm."
In the light of the concerns expressed in the US, the UAE company said: "DP World will segregate P&O's US operations while it engages in further consultations with the Bush administration and as appropriate congressional leadership and relevant port authorities to address concerns over future security arrangements at P&O's US ports."
Bush has threatened to veto any legislation passed in Congress to block the deal.