The plans are reportedly on hold while Mr Netanyahu waits for approval from Donald Trump.
A spokesperson for Mr Johnson said on Monday: “The Prime Minister spoke to Benjamin Netanyahu, Prime Minister of Israel, this evening.
“The Prime Minister set out his concerns about plans to annex parts of the West Bank unilaterally and cautioned that this would set back the prospects for peace in the region.
“He reiterated his personal support for Israel and urged Prime Minister Netanyahu to return to negotiations with the Palestinians.
“The leaders also underlined their ongoing commitment to UK-Israel trade and discussed the global response to coronavirus, agreeing to continue working together to tackle the pandemic.”
Mr Johnson criticised the planned annexation last week, warning that the move would be illegal and harm relations in the Middle East.
Writing in the Yedioth Ahronoth newspaper, he said: “Annexation would put in jeopardy the progress that Israel has made in improving relationships with the Arab and Muslim world.
“But however strong their interest in a different kind of relationship with Israel, annexation would inevitably set back these opportunities and constrain potential Arab partners. Israel’s enemies would seize upon it, and use it against those in the Middle East who want to see progress.
“Annexation would represent a violation of international law. It would also be a gift to those who want to perpetuate the old stories about Israel.
“I profoundly hope that annexation does not go ahead. If it does, the UK will not recognise any changes to the 1967 lines, except those agreed between both parties.”
The UN secretary-general, the EU and several Arab states have all said the annexation would go against international law and undermine the goal of creating a viable independent Palestine state alongside Israel.
In the 1967 Middle East war, Israel seized the West Bank from Jordan. The international community considers Israel’s more than 210 settlements to be illegal.