Merafhe, who spoke on Sunday and whose country has emerged as the region's foremost critic of President Robert Mugabe's controversial rule, called on southern African leaders to remain engaged in finding a lasting solution to the political impasse in Zimbabwe.
"The Vice President (Merafhe) affirmed that progress in Zimbabwe was very much in Botswana's own self interest, while the current political standoff in that country was having a negative local impact," the office of Botswana President Ian Khama reported.
"In this respect, he noted that there are currently over 1 000 Zimbabwean refugees in Botswana, whose upkeep and general welfare cost government about 1.2 million pula a month."
Zimbabwe's long running crisis has spawned a huge refugee problem in the region with an estimated three million Zimbabweans now living in neighbouring countries - the majority in more prosperous Botswana and South Africa - after fleeing home because of political violence and worsening economic hardships.
According to statistics provided by Botswana's government, Gaborone has since 2005 repatriated over 175 000 illegal immigrants from Zimbabwe while spending 62 million pula building facilities to hold illegal immigrants, feed and transport them back home.
Merafhe noted that a Southern African Development Community (SADC) summit last week ruled that Zimbabwe's rival political leaders urgently form a government of national unity in line with a September 15 power-sharing agreement.
However, the Vice-President said in the event the Zimbabwean parties fail to implement the power-sharing agreement as ordered by SADC, then "it was in the logic of circumstance for democracy to be allowed to take its course through the holding of new elections under international supervision".
A similar call by Khama for fresh elections in Zimbabwe two weeks ago drew an angry response from Harare which accused the Botswana leader of unwarranted interference and said his call for new elections amounted to "extreme provocation".
Mugabe's government subsequently accused Botswana of training youths from opposition leader Morgan Tsvangirai's Movement for Democratic Change (MDC) party to destabilise Zimbabwe.
Gaborone dismissed the charge and has asked SADC's Organ on Politics, Defence and Security as well as the Zimbabwean government to undertake a fact-finding mission to Botswana to probe the allegations.
Relations between Zimbabwe and Botswana have long been strained with the Gaborone authorities accusing illegal Zimbabwean immigrants of stoking crime in their country while Mugabe's government accuses Botswana of ill-treating Zimbabweans.
Zimbabwe has suffered a severe political and economic crisis since 2000.
Hopes that a power-sharing government would help ease the political situation and allow the country to focus on tackling the economic crisis look dim after the opposition refused to join the unity government before outstanding issues in power-sharing talks with Mugabe are resolved.