Iran has branded a recent US supreme court order to reinstate elements of Donald Trump’s travel ban racist and unfair, as Washington prepares to begin implementation of the divisive policy on Thursday.

Trump’s travel ban targets visitors from six Muslim majority countries, including Iran, and temporarily suspends resettlement of refugees in the US. On Monday, the supreme court partially lifted two lower court injunctions blocking the ban, allowing parts of it to come into effect over the summer before a full hearing in autumn.

Iranian foreign ministry spokesman Bahram Ghasemi, according to Iranian state TV, said the ruling was “an indication of the decision of the leaders of that country to discriminate against Muslims.” He went on: “It’s regrettable that the American government, because of their economic and commercial short-sightedness, have closed their eyes to the main perpetrators of terrorism in America.” He did not elaborate.

On Tuesday, Iranian foreign minister Mohammad Javad Zarif told reporters in Germany that the ban, which Trump argues is necessary on national security grounds, would “not help fight terrorism”.

Zarif said: “We always believed that the Muslim ban that President Trump imposed soon after assuming office had no basis in facts.”

The comments came as officials in the US scrambled to ready themselves for the order’s partial implementation on Thursday, 72 hours after the supreme court ruling.

Trump’s executive order, a streamlined version of a chaotically implemented first ban from January, blocks visa applications from the six targeted countries, which also include Libya, Syria, Somalia, Sudan, and Yemen, for 90 days and suspends resettlement of refugees to the US for 120 days. The order also allows for individuals to apply for waivers if an application is denied.

The decision from the nation’s highest court on Monday says the ban can only apply to individuals who lack a “credible claim of a bona fide relationship with a person or entity in the United States”. Although the court provided some guidance on the definition of such a “credible claim”, advocates argue that this could remain open to interpretation and lead to potential confusion at airports on Thursday.

US Customs and Border Protection [CBP], the federal agency responsible for implementing the order at the nation’s borders, said on Monday it would provide “clear and sufficient public notice” to travellers affected by the order after consulting other federal department responsible for implementing the ban.

On Wednesday, however, an agency spokeswoman did not comment on whether frontline CBP officers had been guided on how to implement Trump’s ban at the border, and referred the Guardian to the statement issued on Monday.

At a US state department briefing on Tuesday, reporters were told that refugees who currently plan to travel to the US for resettlement would be allowed to enter the country until 6 July under current protocols.

Beyond 6 July, we are not totally certain how that will work because, again, this is in flux US state department

“Beyond 6 July, we are not totally certain how that will work because, again, this is in flux, this is in progress, this is a new development as the supreme court just spoke to this yesterday,” said department spokeswoman Heather Nauert.

Nauert added that department was yet to receive a definition of a “bona fide relationship” with the US.

Trump’s order also issues a cap on the number of refugees arriving the US within the calendar year of 2017, lowering the total number of admissions from 110,000 under the Obama administration, to 50,000. Nauert confirmed that department was already close to reaching 50,000 admissions this year, but those who could prove “bona fide” ties to the US would remain unaffected by the ban or the cap.

Refugee advocates were cautiously optimistic that the condensed version of Trump’s ban would not lead to the chaos of January, after the president’s first order was brought in and quickly blocked by a number of federal courts.

“While we don’t expect that there will be chaos, we do expect that there might be some confusion in the implementation, and we hope that we can work with the government to sort through that and hopefully get the travellers through as quickly as possible,” said Mark Wasef, a senior staff attorney at the International Refugee Assistance Project.

Legal volunteers are expected to be present at major international airports throughout the United States on Thursday. At some locations, volunteers have maintained a presence since Trump’s January order.