It is a taboo for Israeli leaders to give even the slightest hint of favouritism in politics in the United States, Israel’s closest ally. So some Israelis are squirming over a perception that their prime minister is siding with Republican Mitt Romney in the US presidential race, in the belief he will take a harder line on archenemy Iran if elected.

With President Barack Obama holding a narrow lead in opinion polls, Benjamin Netanyahu’s perceived strategy looks risky to Israelis, who fear their alliance with the US could be in trouble if the incumbent wins.

Netanyahu, convinced that Iran is close to developing nuclear weapons, says Tehran must be stopped. Claiming international diplomatic efforts and economic sanctions have failed, Netanyahu says the threat of force must be seriously considered. He has urged Obama to declare “red lines” that would trigger an American attack on Iran’s nuclear facilities, coupling his appeals with veiled threats of a unilateral Israeli attack on Iran.

Obama has rejected these calls, saying diplomacy and US-led sanctions must be given more time and that Iran will never be allowed to obtain nuclear weapons. At the same time, American officials have pressed Israel not to attack unilaterally, a move that could set off regional mayhem just ahead of the November election.

Netanyahu has not backed down. In a message directed at the White House, he recently said: “Those in the international community who refuse to put red lines before Iran don’t have a moral right to place a red light before Israel.”

Israeli leaders have relied on broad bipartisan support in the US for decades, but Netanyahu has had a rocky relationship with Obama, underscored by public differences over Iran. These agreements, coupled with his longstanding friendship with Romney, have created a perception that Netanyahu backs the Republicans.

In interviews on American television this week, the Israeli leader vociferously denied he is meddling in Obama’s re-election campaign and said he appreciated the importance of American support.

“God, I’m not going to be drawn into the American election,” Netanyahu told NBC television. “What’s guiding my statements is not the American political calendar, but the Iranian nuclear calendar.”

Obama aides have sought to portray relations with Netanyahu as unshaken. But privately, American officials have grumbled about a perception that Netanyahu is telling Obama what to do.

When Netanyahu travels to New York this week, he likely won’t even see Obama. The US president turned down a request for a meeting, citing scheduling issues. A subsequent phone conversation appears to have done little to ease tensions.

Differences between the men run deep.

Soon after Obama and Netanyahu both took office in early 2009, they clashed over Israeli settlements in the West Bank. Under American pressure, Netanyahu reluctantly agreed to slow down settlement construction for nine months in order to restart peace talks with the Palestinians. When the moratorium expired, Netanyahu refused Obama’s appeals to extend it, and a fresh round of peace talks quickly collapsed.

In one tense encounter, Netanyahu appeared to lecture Obama on the pitfalls of peacemaking as they sat in front of reporters in the Oval Office. During that same trip to Washington, Netanyahu was warmly welcomed in a speech to a joint session of Congress, sending a message that the Israeli leader maintained strong support on Capitol Hill.

The US-educated Netanyahu thinks like a Republican on many key issues, whether it be his support for free-market capitalism and disdain for big government, or his security-first approach to foreign policy. Obama’s first major foreign policy act, reaching out to the Muslim world in a landmark speech in Cairo while failing to visit neighbouring Israel, is still seen as an insult by many Israelis.

Netanyahu’s friendship with Romney goes back to the 1970s, when they worked together at a Boston investment firm. During the campaign, Romney has accused Obama of throwing Israel “under the bus.” And in comments to a closed fundraiser that were captured on videotape, Romney sounded as if he had received many of his talking points directly from Netanyahu as he listed reasons why peace between Israel and the Palestinians isn’t possible.

Few believe any damage in relations is irreversible, and officials in both countries say defence ties remain close. Pinkas, the former Israeli diplomat, said the Iranian nuclear programme is so critical that the countries will find a way to work together. He suggested that Netanyahu move quickly in the coming months to repair his relationship with Obama, either through a face-to-face meeting or quiet “back channel” discussions.

Netanyahu is required to call new elections in the next year or so. Many analysts believe he will do so much sooner, perhaps by the end of the year. Standing strong in the face of American pressure would play well to his hard-line Likud Party.